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Changeset 0:d9f4c141d88a (2018-09-25)

Next changeset 1:cd256484eb1a (2018-09-28)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1

added:
flye.xml
macros.xml
test-data/E.coli_PacBio_40x_first_1K_reads.fasta
test-data/E.coli_PacBio_40x_first_200_reads.fasta
test-data/Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta
test-data/result1_assembly_graph.dot
test-data/result1_assembly_info.txt
test-data/result1_contigs.fasta
test-data/result1_scaffolds.fasta
test-data/result2_assembly_graph.dot
test-data/result2_assembly_info.txt
test-data/result2_contigs.fasta
test-data/result2_scaffolds.fasta
test-data/result3_contigs.fasta
test-data/result3_scaffolds.fasta

diff -r 000000000000 -r d9f4c141d88a flye.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flye.xml Tue Sep 25 05:24:27 2018 -0400

[

@@ -0,0 +1,99 @@
+<tool id="flye" name="Assembly" version="2.3.5">
+    <description>of long and error-prone reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <version_command>flye --version</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+
+    #for $counter, $input in enumerate($inputs):
+        ln -s '$input' ./input_${counter}.${input.ext} &&
+    #end for
+
+    flye
+    $mode
+    #for $counter, $input in enumerate($inputs):
+        ./input_${counter}.${input.ext}
+    #end for
+
+    -o out_dir
+    -g '$g'
+    -t \${GALAXY_SLOTS:-4}
+    -i $i
+    #if $m:
+        -m '$m'
+    #end if
+    2>&1
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads" />
+        <param name="mode" type="select" label="Mode">
+            <option value="--nano-raw">Nanopore raw</option>
+            <option value="--nano-corr">Nanopore corrected</option>
+            <option value="--pacbio-raw">PacBio raw</option>
+            <option value="--pacbio-corr">PacBio corrected</option>
+            <option value="--subassemblies">high-quality contig-like input</option>
+        </param>
+        <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
+            <validator type="regex" message="Genome size must be a float  or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
+        </param>
+        <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
+        <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
+    </inputs>
+    <outputs>
+        <data name="contigs" format="fasta" from_work_dir="out_dir/contigs.fasta" label="${tool.name} on ${on_string} (contigs)"/>
+        <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/>
+        <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
+        <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.dot" label="${tool.name} on ${on_string} (assembly_graph)"/>
+        <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/>
+            <param name="mode" value="--pacbio-raw"/>
+            <param name="g" value="1m"/>
+            <output name="contigs" file="result1_contigs.fasta" ftype="fasta"/>
+            <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta"/>
+            <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular"/>
+            <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="inputs" ftype="fasta" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
+            <param name="mode" value="--nano-raw"/>
+            <param name="g" value="100000"/>
+            <output name="contigs" file="result2_contigs.fasta" ftype="fasta"/>
+            <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta"/>
+            <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular"/>
+            <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/>
+            <param name="mode" value="--pacbio-raw"/>
+            <param name="g" value="1.1m"/>
+            <param name="i" value="2"/>
+            <output name="contigs" file="result3_contigs.fasta" ftype="fasta"/>
+            <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Input reads could be in FASTA or FASTQ format, uncompressed
+or compressed with gz. Currenlty, raw and corrected reads
+from PacBio and ONT are supported. The expected error rates are
+<30% for raw and <2% for corrected reads. Additionally,
+--subassemblies option performs a consensus assembly of multiple
+sets of high-quality contigs. You may specify multiple
+files with reads (separated by spaces). Mixing different read
+types is not yet supported.
+
+You must provide an estimate of the genome size as input,
+which is used for solid k-mers selection. The estimate could
+be rough (e.g. withing 0.5x-2x range) and does not affect
+the other assembly stages. Standard size modificators are
+supported (e.g. 5m or 2.6g).
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>

diff -r 000000000000 -r d9f4c141d88a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Tue Sep 25 05:24:27 2018 -0400

@@ -0,0 +1,23 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+        <requirement type="package" version="2.3.5">flye</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1073/pnas.1604560113</citation>
+            <citation type="bibtex">
+@misc{githubFlye,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {Flye},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/fenderglass/Flye},
+}</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file

diff -r 000000000000 -r d9f4c141d88a test-data/E.coli_PacBio_40x_first_1K_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/E.coli_PacBio_40x_first_1K_reads.fasta Tue Sep 25 05:24:27 2018 -0400

b'@@ -0,0 +1,115822 @@\n+>m141013_011508_sherri_c100709962550000001823135904221533_s1_p0/29/0_6709 RQ=0.843\n+aaacccacccaacccaagggaaaaaaaaggaaggggaagaaaagattttaaataaatggggggggtttgcccccggttgg\n+aagcgggggacccccaaaccggggagtgggaaaataccgggtttttatttgcgaaaaagctttgggcgaggatctccttt\n+tcatcggggccccggggttaaggtccaacttttccaccgcttcgctttccacgccggcccctgggccgcaaagttttctt\n+gtggaatgtaaaaaacacaaaatactggcctggtttgtgttttttttccagtttttttcgatcccaagaataccttcgcg\n+gttgattttcgctttaatggtttaccggtcagcgggagccaggaagacgccgcatgccgacccgggcaggatgccgccgt\n+gaaaccgtggcagacgggattaaacgcgaatggtcgttgcgcgaagtatttcccggccaaaactgcgcgccaagaccgag\n+tttctggccctcttccagcagttcctgttcccgctggaaacatcgcggaacgcctgaccatgttttcgttcccttccgtc\n+ggcagttcaatcgtaatagtggagcgcttgctaacttgacggtttttcaggttggttttttccgccagacgtatccgccc\n+aatcacaaacgcgatatgggtagcggccgggcaggctgcagtaccgagggtcgcattttttctcgccgaggagtttttca\n+gtttggccggggaagtccagcagcggctttggtttcctggtagagatacgttttgttggcagagccggccgcttttcgca\n+acggcaaggaattgtagctcatcgccatctaccgcgtacaaggtcgatttgcgcagggcaggttagtggccggtgtttga\n+cctctttgtacatgtccagcgccgcattctgtgaatagcgcaggtttatctatcttcgatataggtgttatagaacgcct\n+ttcgacagcgtttctttgcttcatcaccttacccatccgctgcttggaatagtttcgaggccgccggtccacacgcgctg\n+gcctttttaccgacgatgatcgcggtgcgggtatgctctggcaggtcggcagcacgccttttggcggcgatttcggagtt\n+ttttaagattgcagcggccacgtacttgtcgtttgcttgggcttctggatcggtgaagggccgcaacctgttttctggtg\n+tgccggccggaggcagtaaaagaagcgtcgtgacagggcttgctgcgcgccagcagggtcagggcttctggttccacgct\n+ttcagggatggtttcgccgtcgaagtcggcaacgctaacgtaatcggaagtgagtagatagttattgcggtaatttggtc\n+tttccccatcgggaaaggttgcctggtagataaagggttttgttttgacatagcttccagcctgttacctaatatagata\n+tttgtgtttgtattcgaaaatggcgtgggccgcggtagtcacgggcgcacgcaaagtgcatttataagaacgcgtacatc\n+gcggcgtaaagatccagcgaagacgcacgatacgctcacaccaatcaaaccccggcagaataaagctgtggttgatgacg\n+agcctgactcggcatggggtggtggcccggaacggtcaaactgaatcgctgcgcagatcgctcgataagtccggcaggat\n+gttaataatccgtagcaagccggtgctgacgccacgatggtatgccggactcaacgcgatcgccaagcggcgaaccggaa\n+caatcgccgccaggcgcggccgcaagcctgagagtttaacaacttgagaaaccagcagcagaaacaaagtggccatagcc\n+cacggaatactctttcaccattttcacccagtacgccctgaattccagacattgcgcgacgaaacatggtttctaggcgc\n+caatccattcataccgtacaccgccacgatggcgatcataaccgggaacggaagacttcgtttttttgagatagacgcgg\n+gattggttttggtcaggagataacttaatcagcgccccggtcagccagcataaacatcttgaactaactcagtaacatcc\n+gacagcgttttggccgccggaagggatggacgcaggtcagaatcagcaccaggaagggcggactaacaggcggatttgcc\n+ccgaggaaagggcccattgccagtccagttgcttttcggcagttttttatccagcataagcgtcgcggtatcaccgtaaa\n+catactcacggttgtcccgttttccggtacggagagttgaatttctgggaactcttcgtctttaaaatccagatcttgta\n+cgcgcggacgcagctgaacggataaccgatacggccaggataccggattaacgtcgatgggaatggtgatgtgccaagca\n+gatcgaggaactcagatgggcgaccatcaaggtgacatttacccgccagcatcgcagccagagaacactgaccggcaacc\n+cgacagcgcggatctggcgataatccgccgcatctgtgcaccgatagaacttgcgccagtcgacgttccggacggatgtt\n+gttcttaatggcggacgtcgtagatgatcggcatgaatggttgtaaaccacatgacccgtaccacaaaagaatggtcagt\n+gtaccaggtccacgaaaacggggcgcgacaatttgggaggaacatatttttcgtggttgcggcgcagcagccttcctcgc\n+aatttgcagatgacatccaagaccgccgcgaaagcttgcaaggtcgccgatgccgccaccagcggcaatgataaccaggc\n+atgaccctcaactggtggtttctggctgaaggtggaagacgaagaccagaatgaccagaccgataaccgcctaataaacc\n+cagcgcgataccaccttttctggcacccataaaacagacatatcagtattagaaataagttggatagtaaataacatgtg\n+gtgaatcgctcgcgataatcctccgtttaaattttttgctgatagatcacagtcacgttctgttttgtatgacatgtttt\n+tcagagcgctgactaaataatccgttttggtcgttacgcggggctttagcaaaattaatccctcacagtggaatattggc\n+tgattaaagcagcggcaaatttaatgcactgtagataagcggcttttttcagagagaaagactctctggcgatgggttta\n+tagttttgtactgcgcagatgttaattggttttgtttggctggcttaatgttattgatatttatcggtctatattttttg\n+ttctcacgggcagatgtcattaggttttatagattaatctgatctacccattttgtgggtaaaaaaattacacataatgc\n+ggtgtggacataatagttaattaactttttgttagcgtttttgaaatttaaaacaacgggttcacctgaagaagatatta\n+aatttttagcgctgatggagaggaaattatattggatctggacagagattttactgatgaaggatgtaacttgtgccagg\n+ggtatttttgtcattacggtaataattatttactttacagctaacgcaagcgatccgttattggaatattgttttcagta\n+gtggaagtagtggttctgcctgaataacggtaacgtaaactgacgggcccgtgacgcctaaatggatagctggtggaaca\n+cgaatgtggagtttgaccagccagatgaaggtatttaggcaggtaaacacggcgaatgttaaactcgttgggctgcttcg\n+tcgggttgaaaatttcacatagtccctgatgcgcgtcca'..b'g\n+catgcacgatgcaaagcgatgcgcgcagatcgcgccgcgcgtgcaggcgttttctacggggatcatcagccactatttca\n+gggacaaaaatggtcttgctggaaagggcaaccatgcggcgcatatcaccagtcagctgcgtgacgcgttttgaatcgat\n+tacatgcacttccgcagggcagtgcagagcagcgcgattacagggattgttggcggaaacttcgatgaaccgcaggtgaa\n+ggcagtgggcggcgattgaaacctggctgcgtttctggccagcagtatggctcagcgcgatgctctatcgtttacagcag\n+tcagcagcgcgcccgcttgctgtcgattctgtgagcgagtttcgtgcgcgcaattgcgcgcgaaacaggcaccggaagcg\n+ggctaggctggccgacgctgattgatgggcttatggctgcgcgcgctgctgagcgcaaccgctggtaccgcgcggctaga\n+ttccctgacccgccacttgatcactcagcatctacccaccgattacccggaggagacgtgatgtccgaaatggcagaaag\n+cagctttatatacatggtggttatcctcgccaccagcgtcgcagccttcgagaccattaacccggccaacggtaacgtgc\n+tggcgacgcgtgcaggcgccggggcgcgaggattgtcgatcgcgccgtgaaaagcgccagcaggggcaaaaaatctggcg\n+tcgttatgaaccgccatggaggcgctcggtattctgcgtcgccgttgatattgctgtcgtgaacgcaattgaacgaactc\n+gcaaaactggaaaccctcgacaccggaaaagcaatattcggaaacctggcaccgtcgatatcgttacgccggtgcggacg\n+tgctggagtactagcgcgggctgatcccgggcgctgggaaggcagccagatccccgttggcgtgaaacgtcctttgtgta\n+atagcccgccgcgaacgcgctgggggttagtggcagggattggc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diff -r 000000000000 -r d9f4c141d88a test-data/E.coli_PacBio_40x_first_200_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/E.coli_PacBio_40x_first_200_reads.fasta Tue Sep 25 05:24:27 2018 -0400

b'@@ -0,0 +1,24342 @@\n+>m141013_011508_sherri_c100709962550000001823135904221533_s1_p0/29/0_6709 RQ=0.843\n+aaacccacccaacccaagggaaaaaaaaggaaggggaagaaaagattttaaataaatggggggggtttgcccccggttgg\n+aagcgggggacccccaaaccggggagtgggaaaataccgggtttttatttgcgaaaaagctttgggcgaggatctccttt\n+tcatcggggccccggggttaaggtccaacttttccaccgcttcgctttccacgccggcccctgggccgcaaagttttctt\n+gtggaatgtaaaaaacacaaaatactggcctggtttgtgttttttttccagtttttttcgatcccaagaataccttcgcg\n+gttgattttcgctttaatggtttaccggtcagcgggagccaggaagacgccgcatgccgacccgggcaggatgccgccgt\n+gaaaccgtggcagacgggattaaacgcgaatggtcgttgcgcgaagtatttcccggccaaaactgcgcgccaagaccgag\n+tttctggccctcttccagcagttcctgttcccgctggaaacatcgcggaacgcctgaccatgttttcgttcccttccgtc\n+ggcagttcaatcgtaatagtggagcgcttgctaacttgacggtttttcaggttggttttttccgccagacgtatccgccc\n+aatcacaaacgcgatatgggtagcggccgggcaggctgcagtaccgagggtcgcattttttctcgccgaggagtttttca\n+gtttggccggggaagtccagcagcggctttggtttcctggtagagatacgttttgttggcagagccggccgcttttcgca\n+acggcaaggaattgtagctcatcgccatctaccgcgtacaaggtcgatttgcgcagggcaggttagtggccggtgtttga\n+cctctttgtacatgtccagcgccgcattctgtgaatagcgcaggtttatctatcttcgatataggtgttatagaacgcct\n+ttcgacagcgtttctttgcttcatcaccttacccatccgctgcttggaatagtttcgaggccgccggtccacacgcgctg\n+gcctttttaccgacgatgatcgcggtgcgggtatgctctggcaggtcggcagcacgccttttggcggcgatttcggagtt\n+ttttaagattgcagcggccacgtacttgtcgtttgcttgggcttctggatcggtgaagggccgcaacctgttttctggtg\n+tgccggccggaggcagtaaaagaagcgtcgtgacagggcttgctgcgcgccagcagggtcagggcttctggttccacgct\n+ttcagggatggtttcgccgtcgaagtcggcaacgctaacgtaatcggaagtgagtagatagttattgcggtaatttggtc\n+tttccccatcgggaaaggttgcctggtagataaagggttttgttttgacatagcttccagcctgttacctaatatagata\n+tttgtgtttgtattcgaaaatggcgtgggccgcggtagtcacgggcgcacgcaaagtgcatttataagaacgcgtacatc\n+gcggcgtaaagatccagcgaagacgcacgatacgctcacaccaatcaaaccccggcagaataaagctgtggttgatgacg\n+agcctgactcggcatggggtggtggcccggaacggtcaaactgaatcgctgcgcagatcgctcgataagtccggcaggat\n+gttaataatccgtagcaagccggtgctgacgccacgatggtatgccggactcaacgcgatcgccaagcggcgaaccggaa\n+caatcgccgccaggcgcggccgcaagcctgagagtttaacaacttgagaaaccagcagcagaaacaaagtggccatagcc\n+cacggaatactctttcaccattttcacccagtacgccctgaattccagacattgcgcgacgaaacatggtttctaggcgc\n+caatccattcataccgtacaccgccacgatggcgatcataaccgggaacggaagacttcgtttttttgagatagacgcgg\n+gattggttttggtcaggagataacttaatcagcgccccggtcagccagcataaacatcttgaactaactcagtaacatcc\n+gacagcgttttggccgccggaagggatggacgcaggtcagaatcagcaccaggaagggcggactaacaggcggatttgcc\n+ccgaggaaagggcccattgccagtccagttgcttttcggcagttttttatccagcataagcgtcgcggtatcaccgtaaa\n+catactcacggttgtcccgttttccggtacggagagttgaatttctgggaactcttcgtctttaaaatccagatcttgta\n+cgcgcggacgcagctgaacggataaccgatacggccaggataccggattaacgtcgatgggaatggtgatgtgccaagca\n+gatcgaggaactcagatgggcgaccatcaaggtgacatttacccgccagcatcgcagccagagaacactgaccggcaacc\n+cgacagcgcggatctggcgataatccgccgcatctgtgcaccgatagaacttgcgccagtcgacgttccggacggatgtt\n+gttcttaatggcggacgtcgtagatgatcggcatgaatggttgtaaaccacatgacccgtaccacaaaagaatggtcagt\n+gtaccaggtccacgaaaacggggcgcgacaatttgggaggaacatatttttcgtggttgcggcgcagcagccttcctcgc\n+aatttgcagatgacatccaagaccgccgcgaaagcttgcaaggtcgccgatgccgccaccagcggcaatgataaccaggc\n+atgaccctcaactggtggtttctggctgaaggtggaagacgaagaccagaatgaccagaccgataaccgcctaataaacc\n+cagcgcgataccaccttttctggcacccataaaacagacatatcagtattagaaataagttggatagtaaataacatgtg\n+gtgaatcgctcgcgataatcctccgtttaaattttttgctgatagatcacagtcacgttctgttttgtatgacatgtttt\n+tcagagcgctgactaaataatccgttttggtcgttacgcggggctttagcaaaattaatccctcacagtggaatattggc\n+tgattaaagcagcggcaaatttaatgcactgtagataagcggcttttttcagagagaaagactctctggcgatgggttta\n+tagttttgtactgcgcagatgttaattggttttgtttggctggcttaatgttattgatatttatcggtctatattttttg\n+ttctcacgggcagatgtcattaggttttatagattaatctgatctacccattttgtgggtaaaaaaattacacataatgc\n+ggtgtggacataatagttaattaactttttgttagcgtttttgaaatttaaaacaacgggttcacctgaagaagatatta\n+aatttttagcgctgatggagaggaaattatattggatctggacagagattttactgatgaaggatgtaacttgtgccagg\n+ggtatttttgtcattacggtaataattatttactttacagctaacgcaagcgatccgttattggaatattgttttcagta\n+gtggaagtagtggttctgcctgaataacggtaacgtaaactgacgggcccgtgacgcctaaatggatagctggtggaaca\n+cgaatgtggagtttgaccagccagatgaaggtatttaggcaggtaaacacggcgaatgttaaactcgttgggctgcttcg\n+tcgggttgaaaatttcacatagtccctgatgcgcgtccaa'..b'ggcacaggggcgacaccattttgatgttgaacgcctttcgatgcccgctgggcttacaacgtgtgatggt\n+ggtggcgtggcgaactgaagtttgaaaacttcaacgccggcgtcggtcaattataaaattgtcggtaaaaatgttcatcc\n+gggccggcgaaggagtgatggtaatgcgctgtcgctggcggcacgtaattcattgcggaagtttccggcgatgaaagccc\n+ggcaaattgacagaaggctatgaaggtttctattcactggcgagcatgaaaggcacgcgttgaacggcgcgatatgcact\n+acatccatcgcgtgatttcgacgtaaacagttttgaagcgcgtaaacgtaaaagatgagaatcgccaataaaagtgggca\n+aaggtttacatcctgattgctacatgtgaactggtgattgaagacagtttactacaatagcgcgagaaagtggttgagca\n+tccgcatattctcgatatcgcccagcaggcatgcgcgaattgcgctatttgaaaacggcggaactgaaaccgatccgggc\n+ggtgttagccgacgcgccgcagtttgtcgtttatgggaattacccgtggccgaacctgttcactggcggtttacaactac\n+atggaagcatgagttttgtgtgactctggaaggtatggaaaaaagcggtgcaaggtgatcgtccgtattgcgagttaacg\n+ggcgcaacggaagtaagcgaaaagggatgcggcatgtgatgccgatcccggcttaaatccaaactttacccttcgaagaa\n+ccacaataccgctattgaccagcgccgcgagcatcgcgaggaatgggacgatcttcagcgcatcgccaaaattctccgca\n+gtcaagcgcaatgttgctgcgagtgcatccagtgccggacgtggcggaatccgatcttctaaccattggccatacacgtc\n+gtcgccaatgcgcaatacgcgcagaccacccaggcggcaccagcactcacccttgtttcagcgcatcgtagattttcatt\n+ccgctgataaggcggctctgggcggcgcgaataatccagtttcatgacgttgactgggatttaaactcgccaaaccacct\n+tggcctaaagtgttccggctggttgatcaattcgaagcatcatctcacgcagttttatccatctcttgcgcagccacatc\n+cgcaaggatgaagccgcgaggtgggaaatccggatcgctgtaagtagttgcccgcccagttcacgttgcagccacataat\n+cggcaaatccactaatcagttcgcgtatttgggcgcggcgaaagcccacggaaatagtttcatcgcatttttcagcgcgt\n+agccttcatgcgggagatcctggcgggaatataagaatatcacaggctccagctcttcatcgatgatggcttcgacggat\n+cgacctgtaaccgatccggatgtggcagtggctgtttcatttgcaggcttttcgcccactcgccagcgacgacgtccgta\n+gctgaatgataaacacgtgtactgatcgagatcgggccgccccgccgcgggtacagaaaaagaataaatcagatcatcaa\n+tacggccagtccggtaggttcacgtgaaccggtcgcatagcgggcggcggtcgcctcatgccagttggttcactgagcct\n+gtaccagtaatgaccagttggtttccaccgagatgatcgtagctttcgaacgggcgtggcctgaccgctgccatttgcca\n+tcgctggtgactgaccagtcgactgttcaactcgctttcccatgcggccagacccgccaactcgtctggaagatcgggtc\n+aataaaaattattaaagccgcgttttaacaccaccgggcgttctgccagtgacgtcaagaacatctggccagttaaagag\n+tgagttggtatttccatgttaacatccccacaggctgtaatctgcaacgatttataacggatgcttaacgtaatgcgtga\n+aagtatggcatatttaattcatctttcggcgcagaatgctggcgagccccaaaatcacctccatcccgcaccgccggcca\n+gcatgcctctctccggcgacgattttacctcatattgctgcgtgatttcgcggctcgccaagccctacaccttgccaggg\n+cgtaaagtatcaacccgtttgaccagcggtcgaaaatgacctctgctgctttaaatggaataccggggccatcatcctcg\n+acgacaataaatagagatgctcgtcggtttgccttgcagaaatttcgaccaaactcgaggcaatatttacagcattatcc\n+agcacgttgcccatcactcgacaacaatcgtttctgctcacgggacaaagctgatctctggcgaaatatcgagagagata\n+ttgaccctttgcgttggatacatctttgttcagccgctgtggtgagattggtccagcagtggggcgaccgatgcagctcg\n+cggctgagcatgtcccccgccgcgcataatggcacgatgcaggtaagtagccatttgcctgtgaatgcggctgatttggc\n+tccagcataccggctcagcatcactgacgtcatttttccactacgcaagagaacgcagcgtactttgccagcaccggcca\n+tgcgtttttcaggactatgggtcaggtcgtgagcggtcgtacggtatttgtcgtaacgttcgcgtttcactttttaacaa\n+ctcggttcaggttttcgtacgcagactgggtcattctcgcgttgtggctgggattgacaattcgcggttatgttctttcc\n+atttcgcggacctcttttggccagggcttcgatggggcgtaaactccaccaggacggcgaccacagcagcggatcactaa\n+acagcagattggcgagagggcacatagataaaccagctccagactcatatggaactttttagcttccaccgaatggtatc\n+caccaccacaaggtgtaattttgcaatcccgcgatgttgccggtagaacgtttctgccaccgagtgggttccatctccgt\n+cgtcgtcatcagtcttccgcactttcttgaccactgttgctgtaatcagaatgatcgtccactcagcaaggaggctgtat\n+cgtttaacatcgcgcttcaaatttcatgaaaccattcgatttcagccagtcaggctggatcatcttcatcagccagggca\n+gcgtcacgttgcgccataaaaagcttgccgttctcattcataaattagcgcatgtggggggctttggcttgtcgatatat\n+ttcgggtaacctcgacatgcaacttattgttttcccacttcgcagggtatagaacagattgctctcgccacgtaacagcc\n+gaaacgtagtttttaatcgaaactgacgctaatacaccgtcagcgcgaccattccgtaggcaaagcgacaagcacccagt\n+actacgctgccgttgccaacagaaaacgtacccgcagcgaccagagcgggggaaaaaaaagacgcagtaaatttttttca\n+atcagcgcaattcgaacagatagccctggcccgcgaacggtgggtaaattcacttcccttggggatattgtggcctgaat\n+tttttgcggcagacgtcgcatcagtacatcaaaatggtatggcttttcccgcaagctcgctccggatagagtggagcata\n+cagaatctttggctgaccactttggccatattgcgtatcaacgtttccataatagtgtattcgaagcggcggtcagtttg\n+atcaacttcgtcattaatagataacttcaacggcgagagagatcaacctgaaacggggggaggaaatgacgctgtgaagg\n+ccagaccgctattacgccgcattaatgcctgcattcgcgccatcacctcttcaataatgaaacggtttagtt\n'

diff -r 000000000000 -r d9f4c141d88a test-data/Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta Tue Sep 25 05:24:27 2018 -0400

b'@@ -0,0 +1,1000 @@\n+>a019fb87-85b7-495a-b6dc-789a2f8c4572_Basecall_2D_000_2d LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch206_file49_strand_twodirections MAP006/MAP006-1_downloads/pass/LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch206_file49_strand.fast5\n+TACGCATAAGCGCCAAAAGCACGCCGGGCGACCATAATGAGAAGATGCTCACCGCCAGCGTCAACAGTAAGTAGACGATGAGAGCGCCAGGGTAAACAGTTTGCACGGGCCGCGACGAAGGCAGTCGATAATGCCGCCATTGCTGGGATGCTCGCCCCCAGACGCGCATAGGCATAACCGGAAAACATCGCCACAATACCGCCAAAGCAAAGGCGACCCCAGGTCGAGGCTTCCATTAGCAATGCAGCCTGCCCCAGCAGCGCGAAGATCGCCGCCCCCACCATTGCCCCGGATTATCGATGGAAACGACGTTCCAGACCGCGGGTTTGTTACCGTTATTACCTTCCGTGTTTCATCATGTAATAGCAGCCCTTAGTAAACACGTTATAGCCGAAAAATTGCTTAGCGACCGATGCCACCATTTTTGACCGCGAACACTGTTGCCATCTTCGTCCAGCGGTGGTGAGAGAACGCGGCAATTCCCATCACTCCAGGGGACGACCACGCCAGAATACCGCCACCTACACCCGGTTTACGCCCGGTAAACCAACACGATACGCCCAGTCACCGGGAACATACCCAAGACTACAGCCCTTCCATCATCATTTCGTAAGAATGTACGGCACGTTGTCGGCCTGAAGAACGCGTTCCTGCGTCAACGATTCGCACACCACCTGCGCCGCGCTTGTCGCGCCAAGCGTTGCCAGTTCGCTACGTGGTCGAGGAGCCCTTGGAGCACTGACGGGTATACACGTCACAGGCTTCCCATTGCATCACAATAGAGATATCCGGCGGAGTAAGCAGCCAGGCTATGGCCCGGTTATGGAGACTTTATTTGTTTGTTCCGACTGGTTAACTTCGTCAGAGAGCGCTACCTGCTCGCCAGCAGTTTGCTTTGGATATGTAAATTCGCTGCCAGCGTTGTTCAACAGTTTTCAGCGTTAATCAGGCTATCTTAGGCAATAGCGCCAGGATAGATTCACCAGTGGCGGGAAATCGTTTGCCGCGGATGCAACTCTAAGGCGATAACTGAGTTACGGGGCAAGATCCGGTCGGGTCCCCACTAGGGATCTTTGTGTCGTACCGCCTGCGGGCCGCACATCTTCCAACGCAAGGGCTAACGTACAGAGACTTTCGAGATGGATTCCAGTGCAAAGCGTAATCACTGTCACCGCACTACGACGTTGCCATCGCGCAGTACACGATAGCCACTGCCGCCAGTTGACCTGGTACATTCGCCGAAGGGAATGTAATCGGGCATTTTGTCCGCCGTTAAGTGAGTGAGAAATTGGGTGTAAGCCTGATCTGTTACGGAATTGCCTGCTGTAATTTGTTTGCATCTAACAATATTTTCTTGTTAACTCCTTTTATAAGTCTCGGGAGGTAATTCCTCACCGGCTGGTGCCGATTTCAGGCATCCTGATTTAACTTAGCACCGGAGACTTAACTACAGGAAAACACAAAGAGATAAATGTCTAATCCTGATGCAAAAACTGCATCAGCAAATTTTTAATCTTTACGGACTTTTACCGCCTGGTTTATTAATTTCTTGACCTTCCCCTTGCTGAAGGTTTAACCTTTATCACAGCCAGTCAAAACCGTGTGTAAAGGGATGTTTATGTCAAACTATCGACCTGACCCTCTGGACGGCCTGTCTGCGGCGGTCACTGCGTTAAACGCGTGAAAGAAAGTCTTGAACAGCGTCGTCCGGGATGTTGAGCAGGCGGATGTGTCTATCACTGAAGCACGTTACCGGGACTGCCGAACAGGCTCGCTAAATTGAAACCATCAAACAAGCGGGTTATGACGCATCTGTAAGCCACCCAAAGGCTAAACCGCCACAGCCGTGACTGTTATGTT\n+>d74a5991-1f66-4b48-b387-07319ac37082_Basecall_2D_000_2d LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch92_file5_strand_twodirections MAP006/MAP006-1_downloads/pass/LomanLabz_PC_Ecoli_K12_MG1655_20150924_MAP006_1_5005_1_ch92_file5_strand.fast5\n+AAGCTGATATTGCTAGCCATATCGTGGCTACCCATATGAATACTGCCAATCAGATGAAAATGGCGATTGCCGGGGGAGGGTGATATCGATGGCAGGCCAGGTGTAATGATTACCGCGCGACGCATCGGAGGCGACCCGTTTTTACCCGGTGTACAACAGATTACAGGCCACGACCTCCCTTTGTGAAATATCATGCCCTCGCGCGGTGAGGGATGGCGCAATCGGCGATTGGCGACTTGTTTAATGTGTTTGTATGATTCAGTATGTTCTTGCATCGCTATTCACAAGGAAGCAACAGTTAAAACCATGAAACAGGCAACAAGAAAACCGACGACACCACAGCAGATATTCTTCTCTATGAATATCTGGAAGCCTGATTTGAAAATCAATGAGTTAGCAGAGTTGCTGCATGTTCATCGGGTGAGTTTTAGTGCACTGATCAATAACAATCGTAAACTCACTACTCCATATGCATTTTGTCTCCATTTTGGAAACACAGTCGATTTTGGCTAATACCATCCAAGTCGTGGTTGGGAAGTTGAAAACAACATGCGCACCGAGGAAGAATTGGACGGATTGAAACATGTAGGGCTGATTTGGCGCCGTGAAGAGCGTGCAAAAAGGTCGCGTAAGGCCAAACACCTCCATCTCGTAGGCCGGATAAGGCGTTCACGGAGTGCGGCATGAGGCGTGGATCCGAGCTTACCGGTCTTAGGACCCTCCAAACTTGCTGAACTGCGTCTAGCGGATAAGGCGTTTACGCCGCATCCGGCATCCGAGCACCACATTGCCTGATGCGACGCTTACGCGTCTTATCAGGCCTACAAATCCTGTGCCTGAACCGTAGGCCGGATAAGGCGTTTACGGAGCATGAGCGGCATTCCATGCGTCGATGCCAAGTGCGCCACCCTAAAGCAGCGCATCCGCATGATGTACTTATTCCTTCGGGTTTAAACCGCAGCAAACCGGTTGGCGTTACTCACTACGGTAATCGACGCCGAGAGCGCCATTGCCGCTCCGGCGATAGCCCGGGTTAAGCAGTGTTCCAGTGAACGCCAAATACCGGCGGCGACCGGAACCCGCATGATACTGTTGTAGATAAACGCACCGAGCAGGTTCTGCTTCATGTTGTGCAGCCCTTCGCGCGGGAAAGCGAGCGCATCCGCAACGCCCATCAGGCTATGGCGCATCAGGGTAATCGCCGCGGTTCAATGGCAACAATACCTCATGCCACCCATCGCAATGCCGACATCCGCCTGAGCCAGCGCTCCGCGCGTCGTTAATGCCGTCGCCCACCATTGCCACCTGACGTCCTTCACTTTGCAGATGTTATCCAACCTTCATAGTTACTCGTCCGGCTACGCGGTCGCGATCACCTCATCAATCCCTGCTTTCTTTAGGAAGTGCATTGGCGGTGGTTCGCTTATAGAGACGTCAGCTCATCGGCGACTAATCTCAGTTGTATGCAGTTCCGCCACGCTATCACTACGAACACGGATCGCGTACTGCGCACCAGGGCTACTCGCTTTCCCGTCAACCGCAGCACAGGCGTTGCCCCTTGCGAATTGCCTGAGCAGCTGCCTTGGCCACTTCGATAGCTTTG'..b'GGATGATGCCGTTTGCTGTGGCATTACAGAAAACGGGCGAGCGTGCCGCTGGCGGTGAAAGGGCTCATCTGACATTGAGGTGTGGTTACGGGCCACATATGATGCTGGGGTGTTTGTTTGTCTTGTCGGCGGTTATTGGGCTATTTATCTCCTAATACCGCGACGGCGGTGTTACGATGGCTCCGATTGCGCTGGCTGCTGCCAAAACGATGGGGGTGTCGCCGGTGGTCCCATTCGCGATGGTCGTGGCGATGGCAAGCATCCGCCGCCTTTATGACACTCCATTCTTTCACCTGTTAACACACTGGTTTTAGGTCCGGGAAATGCACTTCAGTGATTTGTGAAGTTGGGGGTACCGTTCACCATTATCGTGATGGCGGTTTGTGTATGGGTGTTGACCCCGATGCTATGTTTCCGTTTTGACAAGAGCCTGATGTCGCATCCGGCGCTTATTGCCTGATGCAAGACGCAGACTCCGGCTGCTTACAGCGGTGAATCCTGGCTAATCTCATCGAGCGAAAGATGGAAATGGAACAAATATTTCCATGAAGCATCTAGTCCATCTCCTTGGCTGCGACGCCGCATTCAGCGCGTCGCTGCGAAGTCGGTTTTGCCACGACACAAGAATTCTTTGAGTCTCGTCGGCCGCGAGTTCTTCCAGACATTCAGATATATGCACACAGTGCATTATTCGCCTGTTTCACCAGCGAGATTTTCTTCATCGGGTATGCATGCACTCGTCAATTAACGGCGCAAATATCCCGCAGCTCTTCCGGAACCGTCATCGACCAGTTTTGCTGAGCGATTTTCTCAATAGCCTTGTACTCCTGAGCGATTTGCGAATTGAAGTATTTCACCGGAGTAGGGGGAGCAGTGCCCCCCTTACCCACGTGCCTGAGGCATCGTGGTACATCGCCAGTAAAGCGATACGTTCGGCGTTGACATTACCGCCAAATTTTCGATTTTGATAGCTTGCCAGCGCATGGGCGACCATCGCTACCTGCAAAAACTGTGTTCGCAACATTTTCGTCCCGCACGTTGCGCAGGAGTGGGATGGAGCATTCTTAATGCGTGCCAGGCGGGAGAGAGATGGGCAAAAAATGGCTCTGTTTCATACCTGACCTTACGTATGATGACATCATCAGGTCATTGTGGCGGGATAACGCTGCCGGATGCAATCTCCGGCAGTGAAGTGAGAATTACAGTCGATGATAACCAGAAAAAGGGAAACGCGAACTTGCTAAGACAGCTCATCATCGACACGCGGTAGCGTACAAATGCGGAAACTTAAGCGGCCACGGCCAGTTGAATGCGTCCCTTGCACCAACAGAACTTTTTCCCTGCAACAGGAAATTCGAACCATAGGATTTCTGATCGTCGTGAATGTTAAGCGTTTGGCGTCGATTTTCGGAAGCACTAGAACCCCGAATGTTTCCGCCCGCAGGAAACGCCCGGAATATCGTTGTAATCAGTTCCCCACGCGCGGTTACACGCTGCTCATAACAGATAAAGAATGCCAGGGGTAATAAATTCACTGATGCTCTGGACTATCAGGCCCCGGTCTGAATGGCGTGTTGCGCAGGAACGTTAGCACACAGGCGCATTGAAGCGCAGCCCATTTCCCAGGACCTTCGATGTAGCCTTTGGCGTGTTTTTCGGCCCGTTCAACTCGCAATCGCCACCCCTGACGGAAGCCTGCAACGCGGTACGTTTCGACAGTCCGTTAAAGCATATTCACCAGCATTATCAGGTGCCAGCGGCGACGTGAGTGATGCTCAGCGTCGTAGGAATTTTGTCATAAATTTCATCGGCGACGATGGAGATTATGCTGACGTGCAATCTCCACAATCTCCATTAAAGCTCTTTGGAATATACCGCGCCGGTTGGGTTATTTGGGTTGATAATAACGGATCCCACGCGTACGAGGCGTAATTTAGCGCCGAATATCATCGGAGTCCGGGAACCAGTCAGAGGATTCATCGCAAAGATAATGCACCGCTTTACCGCTGGAAAGCGAAACCGCCGCGGTCCAGAGTGGGTAATCTGGTGCAGGAACCAACATTTCGTCCCCGCTGTTCATAGCAATGCCTTGCATTGCCTGAAAGCAATAAGCTCGAATACACCATTGCCGATGTAAATATCTTCGCAAGTGTAACATCAAGCATGCCACGAGCCTGGTAGTGCTGCATGATGGCTTCACTAGGAGGATAAAGACCTTTGGAATCGGAAAATACCCTTGAGCGAGCTTAACCCATGCGTATCACGTCAACGAGGATTTCATCTGGCGCGTCAAATGGGGCATCGCTGGGTTGCCGATGTTCAGTTTCAGTACCTTGTTACCTTCTTCTTCCAGGCGTTTGCTTCTTTCAGCACCGGACCACGGATGTCATAACAGACATTCTAAATTTGCTGGATTTTCAATGGGGGACATGAATCTTGACCTTTTGCTGTTATCGCGCCACTCCCTGCCGTGGAAGTCAGCTTAGAACAATGTGATAACTCCCCCCAGGACGGTGTTTGAAGACAGGTCTGCAGAATAAGATTTTGCCAGAGGGGAAGGCTCGATTGTGCTGTTAATAACTTAATAATGACAAAATAATGAGGTGTATGCTTTACATGCAATGTTATAGTGAATTGTTCTGATTCTCTTAATTGTAAAGTGTCTGGTTTTATCTTAAAGATAATTGTGAAAATGCCTCATTTAAGAATTCACTAATGAAACGCGATGATTTCCTCATTACGGAGTTTAACTGCGTGGTGATGATTTCGAGGTGTCGCAATGGGGGCAAGTGTGAAACTATTGTTAAGCGGAATTAATGAATGAGGATGATGCTAATTAATTATTATTTAATATTCAAAAGTATTTCTTTTGATGTTGCTTATTAATAAAGAAGATTACTTTGCCTAACATAACATAACTTTGCATCAGATAATTCGCAATGACCCTTATAAATAAAGGTTTTGGGGGTAAAAATGCTCGGATAAATGACGGATTGCTGCTCTTGATGCCTAACTCGATGCTGTTGGTACGTTCCGCGTATGACCAGCGATGATGCTGCACGAGAGTGGAACAAGCATACGGATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTTAATAGATATGCGTCAACCCTGAAGATATATTCTGTGATCTACTTCAGGCATTATAACTGAGAACAATGTGGCTTGGCCTTTTAGTGCAACTCATTGCATTTTTACTTTCGTCCCGGGTTCCGGATGAAACTGCCAGGGAGGCACATTACAAATGAAATTGCTTGTTTGTGTGCACAGCATTAACCAGCTCATGAGCCGCCAGTAATGATAATATGATAAGTGCAAATCGTCCGATAATTAACCTCATGACCTCGGAGGTCAACTTGCTGAGAACATTTGTTGCTGTTGCCGTACGGACATTTTCTGCTGCCGCATGATGCCGCTGTGTCGTACTCAGTCCGCCGTAAGTCAGCAATGCAGCGTCTGGAACAACTTCCGTTGGGAAAGAACTGTTCGCCTCTATTCTGACGGTCGCAACAAACTGTTAAACCTCTGAACATCTCAATTCAATTCTTGGTTACGCCAGGAAAATCCTGCGTTTTAATGGCGGCTTGAGGGCCATCTCATCATTAAGTATTTCAGTAATCTTCAGGGCGTATGGTGTCAACTATCGGTGTGCTTCAGTATCGGAATCTGCCGATACGTGATTAGCTTTTCCTGTTAAATCGCGTGAGTTTCATTTATCCGAAATTAGCCCCTGGGAGATGTCCGCGTTAAAACGGGCATGCCTATGGCAGAAATGCTGGGAATTCTACGAGGAAGTGGATTTGATGGTGTAACCCCATCGTCCTTCAGCGTTTAAGTACGCATTGAACCTGCGTACCTCGCCAACACACTGGTACTGCGCAGCGCAAATACATATTGCAAAAGGCGAGCCGTACGCTTGTATTGCTGGTAGATATGTACACGTTCTGTTTATGTA\n'

diff -r 000000000000 -r d9f4c141d88a test-data/result1_assembly_graph.dot
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result1_assembly_graph.dot Tue Sep 25 05:24:27 2018 -0400

[

@@ -0,0 +1,10 @@
+digraph {
+nodesep = 0.5;
+node [shape = circle, label = "", height = 0.3];
+"0" [style = "filled", fillcolor = "grey"];
+"1" [style = "filled", fillcolor = "grey"];
+"2" [style = "filled", fillcolor = "grey"];
+"3" [style = "filled", fillcolor = "grey"];
+"3" -> "1" [label = "id 1\l32k 2x", color = "black"] ;
+"0" -> "2" [label = "id -1\l32k 2x", color = "black"] ;
+}

diff -r 000000000000 -r d9f4c141d88a test-data/result1_assembly_info.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result1_assembly_info.txt Tue Sep 25 05:24:27 2018 -0400

@@ -0,0 +1,2 @@
+seq_name length cov. circ. repeat mult. graph_path
+contig_1 32752 1 - - 2 *,1,*

diff -r 000000000000 -r d9f4c141d88a test-data/result1_contigs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result1_contigs.fasta Tue Sep 25 05:24:27 2018 -0400

b'@@ -0,0 +1,547 @@\n+>contig_1\n+ATCGAAATCAGTCGATACCGCAGTGATATATCGTGAACATGGGTGCAACGCTGAGTTACA\n+GACATGCGCCTGGGGAACGGTAGGGAAATGAACCTGGCTGAAGGCGGCTGTGACGCAAAG\n+TAAATTTGTCGATGATAACCGGCCGGTGAAGGTGAATAATGACGCGTAATTTCGTCAATG\n+ATTTGTCGGCAGACGTGAATATACCAGGCAGCTATCTAAAGCCTCATTCAGCAGTACGTT\n+TAGCGACATCTCGCGGGTGGCGGTTATAGCCATGGTGCGGTGTGGAATCCCGCATGGAAC\n+GCGTGCGCTGGTGTGAACAATCGTGCGTTCTGACCATCAACGATAAACTGCGCTCGGCGC\n+AGTTTTCCGTTTACAGATGTTGAATAGGGAAAATCTGGCGGCAAAAAAAGCCCGACCAGT\n+TACGGCGGGAAAACCTCATCCTATGGGAGAACAATGCAATAATGAAAATTGCGGGGTTAT\n+CATCTCCCAGTCATATCCAATACTAACAATAAGTTACTCTACTCAACGCAGCATAAACAT\n+TTGTTTTGTGCGTGGGAACACGCCTTAAGGTGGTAAAGGGCGAGTGGAATAGCAAATGAG\n+CGAGTATCAGCAAGAATACTCCGCGCTTTACCACAACGTGATGAGAGCGCATGAAAACTG\n+CAAGCGCAGAGATAACTCGCCTGCTTGAGATAAATGCGTGCTTTTATCAGCGGCTTTATT\n+TTCAGCTCTTACTGCTTCCGTAGGTCACGTTCAGCTCAAGAATAGAGAAATATCGCCATC\n+TTTTGCATCAAGCTGTACGTCTGTACCGATCTCAGCATCAATTTGCTACGTATTTACAAA\n+TGACCTCAGAATATCCTTTACGCACTGCGGCAGATAATGCGGTTCTGCATCGCTGCGACG\n+GCGTCAGCAAGCAATAATCTGCAGCCGTTCTTTTAGCAATGTTGCTGTGTTTTTCTTGCG\n+CTGCGAGAGAAGAAATCGAGTAATGACCATAACTTATGCCTCTCGAACAAGCGTTGAGGA\n+AGCCTTTCTTCTCCTCTTCAATGACCAGCGGAAAAGGACGTGGTCTTCTCCCAACAGACG\n+TTCTACTACGGTATCTGCGTATGGCTTTACCGCAGCGCGTTAATGTCGAGAATGACCGGT\n+TTCACACCCTGGTTAGAGCGCGCGCAATACTGATTGATCCTCTGGGATGCACGCCGACGA\n+GTTCTGATGCGCAGGATCTCACAGCACATGCTTCGCATGCTCAGCATGTCACCTCGGCTT\n+ACGCGGCCTGCGGTTATAGCGCGTTAACAGCAGGTGCATCTTTAATAGGCTCTTCGCGCC\n+ATTTTCTGCGCGGCGTGATTTCGACGCCAGAATGCCCTAAAATACGTCAGAGTCGCGTAC\n+TGAGGAGACTCCGGTGTTGGTGGTAATAATGCAGCTTCGTCTGCAAAATAGAGTGCGCAT\n+TAACGCACCGGTTTACAATCCTGCGGGGAGGCACAAACGATAAATTCAAAATCCAGCGCT\n+TTCAGATCATCAAGAACTTTGCGACCCTTCACGGCTGAGGTCATCTTTATCGCGTGTTTG\n+CGACTGCCGGCAGAATATAGAGATATTTTCAGTACGCTTTATCTTTAATTAACGTAACGC\n+CTGATTTAGCGTTGCATCGCCTGAATGACGTTGACGAAATCTAGGTAAACGACCCGGCGT\n+CACAACCCATTAATCAGGTCGAGAGTACGCAGGCCGATATCAAAATACTATCACGACAGT\n+TTTGCTTTCCTTCTGGGCCAAACCAGTGGCGATGCCGCGCTGGGAGGTGTCTTACCAAAC\n+ACTTTGCCCGATAAGTAACAACAATAATGCGTGCCATAAGAATTCCTTGTTAAAAAGCCG\n+ATCAATTTAACGGTTGTAACGGTCAATAAGCGTTTTCGACTAACTGCAGTCGCGCCGCTT\n+TGCCATAAAATTCTGCTGCGGATTTGATCACTCAGCCAGTATTCACCTGCGCATGGACAC\n+CAGTTCCGCCATGCAGGTTCGTACAAAATATTTGCGTTTCCCGGTCACGCACTTGCCCCT\n+GCCAGCGCACGACCGCGCATTCATGCCATATGACATGAATGTTCCCATCGGCATCAAGTT\n+CGGCCCCAGCGCCTAACCGTGCTTGTAACAATCAGATCACATTGTGCCGAGCATTAATAC\n+GCTGCACCGGACGCACCGCGGGTCGTATCTATTAAACGCGTTTTTGTGACCGCGTTGTAT\n+TTTTGCGCTGCGGCAGCCTGCGGTGTGTTGGCGCTGGCAACGTGGCGCTTTTTCCCCTTT\n+CCTTCCGTCAGGCATAGGCAGCCCATCTTTTCAATTTCGCTTTAAGTTGCGCATCTTTGC\n+AGCCACTACGCCAATAACCGCGGCAACGCGTTGCCGAAACCGCCTGTATGCATCGCTGAC\n+AGGTTTACCGGTCTTCCAGTGCCTGACGTTGAGTACAACGGGCATGTTTTAAAAATGGCG\n+GGGCCTGAGCGATTTGTCTTCCAGCGCCTGATGGACTAACCTTAGGTTCTGCCTCATGCA\n+GATCGAAAAGCCCACAGATAAAGGGAAGCTACTGCCTTTTTCAAGCTGCGATTGGCGTGT\n+TTGACATCCTGGCCTTATCGCAATTAGCTATTAATCATCGCCACGCGCGCGATGATGTGC\n+CGACGACTATATAGGCATGTTATAGTCTGGATTATTTTGCAGGCAAGTCACCCTCCCATT\n+TATTCAGAGTAAAAGTCGTATCTGTGATAAATGGCGCTGATTCATAGCTTAAAAAATCCC\n+TTGTCAATCAACCCATTGCCGTCGTACCGGTTTGATTGTTCTTATTTACGCTTCCTTTTT\n+CCGCACCCTAATCGTGCACAGCATCTCCAGACCTGTTTAAATATCCAGTATGGAGGGGCA\n+AGTGTTATCACCACGCCAGCGCTTTCTTACTTTCCATTTTTTGCGCATGCATTAAAGAAC\n+ACGATCGCTTATCTTAATATCCGCCACAGAATTGCTCTATCATAGCAAACCGCAGAAGAC\n+GTCTGATACTTCGGTCAGCGTCATCGTAACTCGTCAGGTCAGCGGGTTTTGATTACGCGA\n+TTGATGATGACATGACGCATAAGTGTCTGTACGCGTTGGCATTATCAGGATGTGCTATGA\n+ATATATGATGCGTATTTTTATATATCGGTATTGTCAGGTGACACTGTGGGATGCCATGTT\n+CTCATCAATGGCGTCTGGGAAATGACGCTGGCGGACTTCAATCTCGGCGTGCGGCGTTGT\n+TTGCGACGCCGTATATTTGTGTGAACTCAGTATGGGCATTGCCCAGAGTTAACAAGCGAA\n+ATATCTCGGCGAGAAAAGCCGCTGAAAACCTTACAATCATACCAGGCTACGATCCCAGCG\n+AATTTACATCGCTACCGGTGTATTTGCGATGTTAAAGAAAAATTATGTCGTGATGATCGT\n+TATTTTGGGTGTGGATGGTAGCGGAGTGGAAAAATCAATCAAACCACCACAAAGATGTTA\n+TTTATGTGTCGTGAGTGATGTCTTGTTTACATTATGTTCTTATTCGTCATTAACCTCTTG\n+AGCGACAGAGAGGAGTGGGGCATTAACGTTTATGACGGGAGAGTCCCGTCGTTGACATTT\n+ACTTAATTTTGAATATCGACGTTTATATTTTTAGTTTTGTTTTTACGGGCGTCGTTTCGG\n+TTTGCAACACTCGCAGCTCATATTTGCCAGAAGCAGGGAGTGAGTATTGTCCCGTGACTA\n+TCGAGTTCTGGGGAATATCTGGATAAATCAACTGGAATCATCGATTCTGGCCCGAAGAGG\n+TAAGTATCAGCGCCTTCATTAGAGATACTCTCACATGCACTTTCTGACCTTTTTGGCAAG\n+A'..b'AGAAGCAACCTTTGAAAGCCAGCACCAGTTTATTATGC\n+GGTGATAACCCTTAAACCATAATAGAACGCAGGAACCAGCTTTATTTTGTGTGCTCCCAT\n+CCTGTGGAACGAGATCGGCAGTGATGACCAGTCAATTAGGAAAAGTCAAAGCCATACCTC\n+GCTCATTATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTTCATTTTGTCGCCAGGC\n+GTCGCGCAGAGCCTTTCCTGTCCTGCTTTTGTGGAGAAGATGGCGTGGCAAGCACTGCCC\n+TAAGTCAGGCAATTCATAATGAAAGCGAAGCTTGCTGCAGAGGTCCTTATAATCCCGTCA\n+ATTGGAGTTATTATTGTGAGCTGCGCTGCGAATTAATTTATGTGGCGATCGCTACGGACA\n+ATGGAAAATGGCCGTCTTGAGTCGGCTGGAAACTGGCACCGGCGGCACGCTGTTCTTGAA\n+AAGATTGAATATCTGGCGTTGAGTTACAGTCTGCTTTGCTTCAGGTTATCAAGCAAGGGG\n+GTTATCACCGCGGACTGGTAATGCCGGCCGTTTTAATACCAATTGATGTCAAAGTGAATT\n+GCAACAACGAACCGCGGACCTCGCAATGCTGTGGCAACCAAAATCGTTTTAGTCGCCACC\n+TGTATTACGCGCTGCCATGCACTTTGAAATTACCATCCCGCCCTCTCGTATGCGGCGTGC\n+AGCATTTCCGTGCGCTGGTGGAATAACAAATACGCAGGCTTGAAAAACGCTTCTCTACGC\n+GGCTCTGAAAATGATGACGTGCCCTCGCCTCGCCTGGTTTCTTGGCATGGCCAGGCAACG\n+ATTTGAACTTTTACAGCTCATCGAGAATCTTGCTCTGAGTAGTGATAAACGGCGCAGTCC\n+CGTCAGTAATTTGCCTGGAAACATCTGTTTACCGCAGGCAGGCGTGACAGATGATGTCAG\n+CGCCACCCGCCCTTTCCACCAGTCTGTCATTTCGCGGAAGTTGAAAAAGAGGAATTATAA\n+CGCAGCCCAGGTACAGGCCGGTCGCATTCAGGAAAGTCGCTTATTGATCGCCCCGCCACT\n+ACGCTGTGGCGGAAAATGAAGGCAAACATGGCATTGATGCAGGGCAGTTAAAGCGCCGGG\n+TATTGAAAGACAGAAACGATTTCTGATACATCAGAGTGATCTGTATTTCATTCCGGCCAC\n+TGCTAACAATTTTCAGCATCGTTTTAAGCTTGTCTATCCCGCCACTTTAAAAAGCTAAGC\n+GATATCCTCCGTTGACTGCTCTGATTCAAAGAGGTTACCTCGGTAATCCGCTTCGAGATA\n+GAAATGATGTGCTTGTTTGTTATACTGGCATGGACTCCCATCGCGTTATTCCAGCCCATT\n+ACCGAAAACCTGTACTTCTCCCGGGAGTTGTTCAAACAGATATTTCGGTATCCCCTGAAA\n+ACTCGCGTATAGCGCCAGTCTCACATAGACATTCAGCTGGCGTTGCCTGCGTATGTCATC\n+CCCAGTTATCATGCTGGCACGCCCCAGCCAGCGATTCGTTAGTGGATTCAGCATGTATAT\n+TTGAAGGCCATTACTCCCCAATCATCTCATTCTGCGCTGGCGTATGTAAGCTGGGTTTGC\n+GGCTCTAATAGAACCCATAACCAGGTAGGGACAGGTTTGACCTCTTGCCCGCTTCCAGGG\n+AGATGCTCATTTCCCATTCGCAGTGCCGTTGCGTTAACTCCGTTTGTTCTGACTGTCCAG\n+TACGTGGAAAAAACTATTTTTCTGCCGCGATGCTTTATAACGAGACGCTGTAAAAACCGT\n+TTTGTGCCATGTAAACTGGCGAACATTCCCCATGTATCTGAACGTGCGGTACGTCGCCTC\n+CGCTATGTCCGCGATGCATGTGTTGAGCCAAATATACAGACGACATACAAACGCATACAT\n+CAGAGAGACGTTATCCCCACCAAACTGTACCGCTGTAAACCACATGTCAAAGCCGCCCTC\n+AGTTTGCCACTGGCAAAGGAAGTCCAGGCTTCCCCATAAAGCGAACCAGATATTACGTCT\n+TTACTCGATTGCGCAGGTCACCCATCCGTGCATCAGCGTACGGTTTTCAACATAGTCAAT\n+AAGTAACCACATTGAGATAATTGCCGCCAGCATCTGCGTCGTGGTGAGCGTTTAGGCGTG\n+AGCGTTCAGGCCGTAGATCGGGCGTTGGCTATGGAGCTGAGCGGGAGCTGTGTGGTTTCA\n+GATTAGAGTCGGTTCCGAACTTTCCCGGCAAGCGTAAAGCTCCCAGTTAGTTCCATTTAC\n+GGGCACATCGTTACAAGATATCCCCCAACCAACCTGAGAAACGCGCTGAACGAGGCCGCC\n+CGTCAGTGGTTTTTACCACTGTCAAACTTTCATTTCCCGTTGTCGCCTCGCTGCCCTGGT\n+TTCGGATAGCAATACGTGATTACCAGCACTACTCCCGCTGATATTCAATTTAAATCCCCT\n+TTATTATTTAACGCCATTACCCTCGCCACACATCAGCACGCATAATAAATGGTATGTTAC\n+GCGCATTCTCTACGTTATGTGCAAGTCCGCAGTTGACCGTGGCTGCAAAATCGACAGTGA\n+ATGCTCAGCGCCAGCGTGTCGAGATTAGAATTACTTGTTAACGTTCCGACGCTGTTATTC\n+ACGCAACGTCCAGTTTCCCCATTGGAACATTATCGCTGAAGGGAGGAACCTGTCCAAAAC\n+CGACCCAGGGGGCATATCCAGATTGATTAGCCCACCTTTGGAAAGAACTGCTACCTTGAT\n+AAGCATACGACCGAGTCGTGAGCGCTGCGGCATAACCATCGTCATGGTGCGTTGCGATGC\n+ATCTGTCGGGTTACTCATATCAATGACCAGAATCGCTCGTGAGGTCGATCTGGCTGTGGT\n+CATGGCATAAATTTCCCCTGGCTCCTTGCCGCGCCGGTGATAGCCAACTGTCTCCGGTTA\n+TCTACGCCGCTGAGAGCCCACCAAACCCAGCGCCAGACTGCCATTACGATCAACTGAATA\n+TCGGTATTTTGCATTTTGACAACAGCGTTGCCGTCTGGCCAGGCACCATAAAGAAACCGC\n+CGAAAAGATCTGATTTCGTTCGCGCCTGCAGAAATGATTATCGCGTCTGAACCACTGGTG\n+ACGAGGCCACCGCCCTGCGCGAAGAAATATGCTATCTGCACCGATAGTGTTGTACCACCA\n+CGGAACTTCGACGCCATTGCCGCGGCTCCAGTTACATCAACAGTGAGTGCATTCGCGCCT\n+AAACTGGCCAAACTCCAGAGGCCGTAGCATTATCGCATTGGTTTAAGTACTGTTTGTTCC\n+GAGATCGACACAGATTTTTCTGTACGTTTTTCCCCATGCGCGTAGCCCTGGAAATCGATT\n+GTCAGTCTGTAGCCGTAAAACGCGCAGCACCAATTGTCGTTATTGCCGTGAACAACCGAT\n+ATAAACACCGTATTCCATCGTCGCGTGATTTTTACTTCCGCTTCCAAGAATCACACTGTT\n+GCCATAGTCATTGATGGTTAGCCTTATAACCGTTCGATTTTCAATGGTGAATGAAGTGGC\n+TGTTAGGTGAAAGCTATTTGCCCAATAATGATGCCGTCAATCGTTACTTCTTAATGTGCT\n+GGCTGTGCCTAAAGTCAGCATTGGTATAGTTCACCAATTAAAGTAATGCCGAGGCAGGAG\n+GTTGACCAACCAACAAATCTACTGTGAGTTCCGGTAAAGCTGTCAGGGAGTTGTTTTTGC\n+CCTGAATAATGAATTTTCCTTTTTGCATTAAATTTTTCCAAGAAAGCCCCCGTCGTTGAA\n+ACATTGACGTGAACCCCAATTTCAATTTTAACCCCCAAGGTTTTGATATTTTTGCCCCAG\n+GGGCCCCGTTTGGTTTCCTTGCGGGGGCCATTTCGTGGCGTGTTCGTGTGTG\n'

diff -r 000000000000 -r d9f4c141d88a test-data/result1_scaffolds.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result1_scaffolds.fasta Tue Sep 25 05:24:27 2018 -0400

diff -r 000000000000 -r d9f4c141d88a test-data/result2_assembly_graph.dot
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result2_assembly_graph.dot Tue Sep 25 05:24:27 2018 -0400

[

@@ -0,0 +1,10 @@
+digraph {
+nodesep = 0.5;
+node [shape = circle, label = "", height = 0.3];
+"0" [style = "filled", fillcolor = "grey"];
+"1" [style = "filled", fillcolor = "grey"];
+"2" [style = "filled", fillcolor = "grey"];
+"3" [style = "filled", fillcolor = "grey"];
+"3" -> "1" [label = "id 1\l21k 2x", color = "black"] ;
+"0" -> "2" [label = "id -1\l21k 2x", color = "black"] ;
+}

diff -r 000000000000 -r d9f4c141d88a test-data/result2_assembly_info.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result2_assembly_info.txt Tue Sep 25 05:24:27 2018 -0400

@@ -0,0 +1,2 @@
+seq_name length cov. circ. repeat mult. graph_path
+contig_1 22450 2 - - 2 *,1,*

diff -r 000000000000 -r d9f4c141d88a test-data/result2_contigs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result2_contigs.fasta Tue Sep 25 05:24:27 2018 -0400

b'@@ -0,0 +1,376 @@\n+>contig_1\n+AAGAAACATAAACAGAACGTCAGTAATCCAGCAAACTGACGGTTACGAAATAGGCGCGGC\n+GACAATAATCTCGTTCTTTCACCACCTCCGGCGTCAGATTCGGATTCACAGCACATCGGG\n+ACCAACGCGTTGGTGCAAACGGATGCGTGGTCCAGTTGTTCCGGGAGTCAACATCTCTAC\n+AGGCTTGAGGACCGCAAATCTCATGGAGCCCCAGTATCGCAGTTTTGTTGCACTATCCCG\n+CGTGTTTCAGGCGAGTGTTCTACCTCGAGTAGCCCGTTACAGAAGTCAAATGCGGCTCTA\n+GCACGAGTCGTAAAGAGGTGGCACCCCGCTAGGAGGGGCTAAGCATTGGCTCAGGAAACT\n+GCTGTATTAAAGAATTCGGTTGTACGGTTCCGCAAGTGAGGTCGGCCTCTAGGTCAAAAG\n+CGTCCAGTAAAGCTAATATTGTCACCGATAAGGTTGATTAACTGCTCGAAGGAAATTTAA\n+AACCATTGAGGAGGATAAGAGCGATATCGCAGTGGACCCAATTAGTGGTTCATTCTATTG\n+CCAGCGACCCATGTATATTCGGAACGTGAGGGTGAAACGTGCCTCCATGTAGAGCTTCAG\n+AGCAGGCATTAGATGCTGGTACAGCCTTTTCGTCGTCATTAATCGGGGTAAGTTACTTAA\n+TGCGACAACAGGATGCGCTTTTCGGGGCAAAATTGAAGAGCGTAGTCATGCGGGCGAACG\n+CCAGTGCGTGCTCGCCAGTAGCGTCGCACTGCATTAAGAAGCCGTTTGCGCCAGCCGTTA\n+AAGAGCGTTTCTGGTTCTACGGTGATAATATGATTTCTGGTGATCCGTGTTGCACCGGAC\n+CCATAGTTCCAGCACTTTCTTCAGTTCTAGTGATAGCGCGCCTGATATGGCTTTCGGAGA\n+TACACCCCAACCCAACGCTTTCATGATAACCGCGATCGGGTGGGAGCCGTTAGACACCAC\n+CCGTTATCATAGGCCACTGGTCAGTTAATTAAATGCAGAGTGCCCCGGCAAACATTTCCT\n+CGCCCCGATAATCGCTCCTGGGAAGAATCATGCTTCCCTGGATGTACGAACGAGAATTGA\n+CCCGCGGCGCCCGCATGGGAGATCGTGCGATTCGTCTGCCAGTTGTGCTTCTTTCGCCGC\n+CTGGTTGTACAACATGCCGTGCGGTTTGACATGACGCATTACGCGCTATCCAGCGCACGG\n+GAAATTCCTTCAGGCGCCACCAATTTTAGATACAGCGTCTGGGCGTAAACGGGGTTTCTG\n+GCGGCATCCAGCTGACGCGCTGCGAAATAAAATTTTCCCCTGTCGGGAAAACTCGGGTGA\n+GCGCCAATCGCGACACCATTTTATTGCTTCCACGCACGCAGCCTGCATGATTTGCGCATC\n+GCCTGCATGAAATCCACAGGCAATATTGTGCAGAGGAAACCAGCGTTAATAGCTCTGCGT\n+TGCTGGCGCATCGCTTCGCCCAAGTTCGGCGTTCAGGTCAATTTTCATTGTGCAGCCGCC\n+ACGCTAATTGTTCAAAAGTAACTGTTGCTGATTTGCCGTGCTTTTTAGTGCCTCTTCCAG\n+TGAACACTGGACAAAATGAATCGGCTGACCGAGCGGCGAATTTGCGCCAGATGGTACATA\n+TCAGCCTCTCAATGATACAGGCAATACGCGGGTAACCACCGGTGGTCTTGCCGTCGTTCA\n+TCAACACAATACTGCTGCCCGTCCTCTTGGCACCTGCACCACGCCCGGTGACAAACCGTG\n+AGATAACAGTTCGCGATCGGTGGTGCGTTTTAAATGTCCCCTGTAAGCGATAGCCATGCG\n+GTTATTTGCGAGCCGGCTGCCAGGCGAACGCCAGAATGCATATCCTGCGAGGCGCGATTG\n+AACTCATGATATTCCGAGTGGCGGCAAGGCGCGAATTGCGGTTGCCCCACAGCAGCTGTT\n+TAACGCCCTGCGCTTCCATAGAATTGGTACGCTTCGATTTGCCAATCGGGAGTCGGTCAC\n+CATCCTTCAGTAAACGGCCTTCCCAGCCCGCCAATCCCCATTTGCAATCACTGCGCGGTG\n+CTGCATGAGCCCATTACCGGCGGAACATCAATACCACCCGCGACCGCCAGATAACTGCGC\n+ATGTAGCGTCTTCGTGGAGGCATCCGTCAGCGTTAAACGCTGGCCTGCTGTTTTCATCGG\n+CAATCGCCAGCCGGTCCAGACGCATTATCATCCAGCCGCGCTGTCGCAACCGGCACCCGT\n+CAGAGCCGAAACCACCCATCAGTTTCGAACCTAACAGTTAACTGACCGAGCGCTGATCTC\n+CATAGCGGGGGCATTGGCGTCATTACCACCAGTATAAGTGCAATGCGTAACGCGGGCATA\n+TCAGTGCGCCGCAGTGGCTGATATCCGACTGGCGAAACCGTGACGACCGCCATCCTGCAC\n+GCGCGTATACATGCCCGCACGAATAATCTTCAGCATACTCCCTCCTTCTGCGTACAAAGC\n+CGCGGAACCTGTCTCCAGGGACGGTGTAATACAAGATGGGTTCGTCACGCGCGCCGGATT\n+AATAAGGACGATGAGTGAGGTATGACCAATCAACTGCCAGCCACCCGGCGTTGCCATAGG\n+GATAAACACCAGTGCGGCCCGCCGATCCCGACAGAACCTGCCGCTGAAAGCCACCGCGGT\n+TCAGCGCCGTGGCGTGTGTAGTTGTTCCGGCAAACTCCCGAGATACGGGAAGCCCGGTTT\n+GAAAACCTAAAAACCAGACCACGTATTCCACGCATAGAGTTATGCAATTCAACAACCTGT\n+TCGCTCAACCCGCAATGCGCCGCGACCACCGCCAAATCCGGTCCGCCTGCCACCGTAAAC\n+CAAGGGGATTTCAATCAAAGCGAGACTCGTGGGTGCCAGCGCCTCGCTCCTCTCCACCAG\n+CGTTGCAAACGCTCTATGGCATCCAGCGCCAGCGACTCAGGATTACGCAAAATCACCGTG\n+ATATTTGTTCCACCTGCCGGGAAACCTGTTCAACCACATTCGGCAATATATCCACCAGAC\n+ACCCTGCGCCAGTCGCCAGGATCCCGGTTTCTGGCTAGCCAGTTCACCGGCGGTTCTCAG\n+TTCCAGCACTACCGCCGTTTCCACCTATCAGATAACAACGCGCTCGTTGCACTTTCACGT\n+GTGGGACTATTATTCGTTATGCAGGATTAGGAATATCAATACAAAGGTCACATCAAGATT\n+TCGTATTTTCACTTCAGCCACTCGCTCAATGCGCGAATACCACCACGTTCAGAGTGGCAG\n+ATGGTGACCTGCAGCATAAAATGCAATCCCTGCTCGCGGGCCTGAATGAATGGTCTTTCA\n+GAAAACTTCGCCAGGACCAACAGGCATCCACGCCAAACGCGGCGGCTATCGATAAAACTT\n+GCCCGCCGCCCGTGCACCAGGCGACGCGCTGGACCACCTCAGTCCGGTATCGCCACACCA\n+TAACGGCTTACGTCCCAGACGCTTTCAATCCAGGAAGCCAGCTGGGCAGTCCCGGCACAG\n+GCAATTGAGTTTCGCCCCACGGCACCAACGGCTCATTTCGCCCATGACCGTGATCCCCCA\n+ATGCGCCGCCAGCTGTGCCATGTTATTGCCCAGCTCAGGATGTGCGTCAAGCGGCAAATG\n+CCAGCCATATAAGGTTGATATCAGGTTTCGCCAGCAACGTTTTTAAACGGTTACGCTTCA\n+TTCCGCGAATGACCGGAGACTCTCTCCTTCCAGAAGTAGCCATGATGCACATGACCGCAT\n+CCGCGCCCAGACGCACTGCCTCATCGAGCAAAGCCTGGGTGCGTGGTGACACCGGTAACA\n+CAATTTTGCACCGTCTCTTTGCCTTCCCACTGCAAACCATTCGGCGTGGTAATCACTAAT\n+C'..b'TGACCGTGAGATGAACTG\n+GAAGCAATATCTTTGTGCCATTCTCGGCCTGAACATGCTGGGGCTGGCGGTGCTGTTTTT\n+ATGTTGCTCGGTTCACACTAGTCTGCCGCTGTAATCTGGACACCAGCAGTTGCCGAGGGC\n+TGTCGTGCGATGATCTGGCGCTGAATACCGCCGTCAGCTTTGTCACCAATACCAACTGGC\n+AATCTTGTAGCGTGAAACCACGTTGAGCTACTTTTCAGCCAGATGGCGGGCTTAACGGTG\n+CAAAACTTTCTTTCTGCCGCCAGCGGGATTGCGGTGATTTTTGCCCTCATCCGTGCGTTT\n+ACCCGCCAGAGCATAGCAGCACGCTGCGGGAATGCCTGCGTACATCCTGCTACGCATCAC\n+GTTATGGGTGCTAGTCCCTCGTGGCGTTGTTGATTGCACGTTTGTATTCAACAAGGTGCG\n+CTGCAAAACTTTCTGCCTTATCAGGCTGTGAATAGCCGTTGAAGGCGCGCAACAGCTGTT\n+ACCCATGGGGCCTGTAGCTTCTCAGGAAGCGATCAAGATGCTCGGTACTAACGGCGGTGG\n+CTTCTTTAATGCCAACTCGTCGCATCCGTTTGAAAACCCCAACCGCACTGACCAACTTCG\n+TGCAGATGCTGGCGATCTTCTTGATCCCAACGGCGCTGCCTTTGCCTTTGGTGAAGTGAT\n+GGGCGATCGCCGCCAGGGGCGCATGTTGCTGTGGGCGATGTCAGTGATTTGTCATCTGCG\n+TAGGCGTGGTGCGTGGTAAGAAGTTCAGGGTAATCCTCATCTGCTGGCACTGGGCACGGA\n+CAGCAGCATCAATATGGAAGGTAAAAGAGCCGTTTGCGTGCTGGTCAGTAGCCTGTTTCG\n+CGTCGTGACGGGCGGCTTCCTGTGGCGCGGTGATTGCGATGCATGATTCGTTTACCGCTC\n+TGCGTGGCATGGTGCCGATGTGGCTGATGCAAATTGGTGAAAGGGTGTTCGGCGGTGTCG\n+GTTCTGAGTCTTTACGCATGATGCTGTTTGTCCTGCTGGCGGTGTTTATTGCCGGGCTGA\n+TGATTGGTCGTACACCGGAATATCTGGGTACAAAATCGACGTACGCGAGATGAAACTGAC\n+TGCACTGGCAATTCTGGTTACCCCGACGCTGGTGCTGATGGGCGCGGCGTTGGCGATGAT\n+GACCGACGCCGGACGGTGAGCGCCATGCTCAACCCTGGCCCGCACTGGTTTTAGCGAAGT\n+GCTGTACGCCGGTGTCATACCCGCCGCTAACAACAACGGCAGCGCTTTGCCGGATCCCAG\n+CGCCAACTCTCCGTTCTGGAACTGTTTACTGGCGTTCTGCATGTTTGTCGGTTGCTTCGG\n+GTGATTATCCCGGTGATGGCAATTGCCGGTTCGCTGGTGAGAGCCAAGCCGCCAGCTCCG\n+GCACATGCTGCCAACGCACGGCCCGCTGTTTGTTGGCCTGTTAATCGGCACCGTGTTGCT\n+GGTTGGCGCACTGACCTTTATCCCTGCCCTGGCGCTTGGTCCCGTGGCGGAATACCTCTC\n+CTGATGATATTGAGTGAGCACTGAATATGAGTCGTAAACAACTGGCGCTATTCGAACCAA\n+CACTTGTCGTTCAGGCAGCTGAAAGAAGCGGTGAAAATTAAACCCGCAGGGCGCAATGGC\n+GCAATCCGGTAGATGTTTATCGTCTGTATCGGCAGTCTGCTGACCACCTGTATTAGCATC\n+GCGATGGCAAGCGGTGCGCAGTGCCCGGCAATGCGCTGTTTAGCGCGGCCGTTGGCTGTG\n+GGTCTGCGATACTGTTAGCTAAGTTTGCCACCGCCGAGTGAGCGTGGCAGAAGGCCGCAG\n+TAAAGCGCAGGCCAACAGTCTGAAAAAGGGGTGACTGCCTTTGCCCGCAAGCTGCGTGAG\n+ACACGAGATATGGCGCTGCGGCGGACAAAGTTCCTTGCCGACCAACTTCGTAAAGGCGAT\n+ATCGTACTGGTAGAAGCTGGCGATATTATCCCCTGCGATGGTGAAGTTATTGAAGGGGGT\n+GCATCGGTCGATGAAAGCGCCAGCCCACCGAAACGGCAACCGTGTGTATCCGTGAATCGC\n+GGCGGCGATTTGCCGCGTCACCACGGCGGCACGTAGCGTGATTCTGGACGCGAGCTGCCC\n+GGTCATTGTAGCGGTATAGACGGCGAGACATGTCTGCATCGCGATCGACTCGCCGATGGT\n+GGAAGTGCGCAGCTGAGGGGACTGAGAACGAATCGCCCTGACCATTCTGGTGGTACATCG\n+CCCGTGACTATCGTCTTTGCTGGCAGCGCCACAGCGCGTGACGGTTTTCACGCTGTGCTG\n+CGCGCGGTACTGCTGCAGTCAGCGTAACGGGTCACTGGTGGCGCTGCTGGTCTGTCTGAG\n+CAACCACAGCAGATGCGCGGCCTGTTGTCATGTCCGGCGTCGCCGGGATGAGCCGGATGA\n+CTAGGCGCGAATGTGATTGCCACCAGCGGACGGGCAGATTCGAGAGCGGCACGGCAGGTG\n+ACGTTGACGGTCCTGCTACTGGATAAAGACCCGGGCACCATCACACTCGGTATAACCGTC\n+AGGCGTCGGAGTTTATCGCGCGCGCAGGCGTGGGATGAAAACAGCGCTGGCTCGACGCTC\n+GGATGACTGGCTTCGCTGAGCGGCGATCCGAAACGCCGGAAGGCCGCAGTATTGTGTGAT\n+CCTCGCCAAGCAGCGTTTTAACCTGCGCGAGCGCGATGTGCAGTCGCTGAGGTTGCCACC\n+TTTGTACCGTTTGATCTGCGCAAAGCCGGTCGAGCGCCGTAATCGACAACCTGACAACGA\n+TGATCGCGTAAAGGTTCTGTCGATGCCATTCGTCGCCATGTTGAGTAGACGCTATTTCAG\n+GTTCAAAGTCGATCCGATGCGCGTCAGGGAGCCACGCCGCTGGTGGTGGAAGGTTCTCGT\n+GTGCTGGGCGTTATCGTGATGAAAGATATCGTCAAAGGCGGTATTAAAGAGCGCTTCGCC\n+CAGCTGCGCAAAATGGAATTAAACGGTGATGATTACCGGCGATAACCGTCCTGACTGCCG\n+CCGCGATTGCGGGCGCGGAAGACCGGTGCGTCGATGATTTTCTCGCCGAAGCGACACCGG\n+AGGCCAAGCTGGCATTGATCCGTCAGTATCAGCGGCGGAAGGTCGTTTGGTAGCGATGAC\n+CGGCGACGGCACCAACGATGCTCCGGCTGGCGCAGGCAGATGTCGCGTGGCGATGAACTC\n+CGGCACCCAGGCGGCGAAAGAGGCGGTAATATGGTCGATCTCGACTCTAACCCGACCAAG\n+TCCGATTTCGAGGTGGTGCACATTGGCAAACAGATGCTGATGACCCGTGAGCTCGCTGAC\n+CACCTTCAGCATTGCCAACGGATGGCGAAGTACTTCGCGATTATTCGTATCGCGGCAACG\n+GTTACGCAAATGCGCTGAACATCATGTGCCTGCATTCGCCCGACTCGGAAGCAATCCTCA\n+TGCGGTGATTTTCGAACTCTACCCTGATTATCGTCTTTTGATTCCCCCGGGCGTTATAAA\n+CCGCTTAGGTTAACGAGGTTCTGCCATGTTGCGCCGGGTAACTTGGATTTACGGTCTGGG\n+TGGGCTGCTGCTGTTTTATCGCACCAAAGTCATTAAGGTGGTTCGAATCGTTTGCGGTCT\n+GGTGTGAGTTTACCATGAGTGGATTACGTTCATTATCAACATTTATCTTCTGTTATTGAT\n+TACTGGCGGCGTTTACCCGCTTCACGGTCACTGGGGCAATGGTGGTTTCCCTGGCAGGCC\n+AATGGTTTCGTTGATTCGTGAATGTAAGCGGCGGTTCGGCATTAATCGGCAGAATTTGTC\n+ACCGGCAACGGCTTTCATGGTCGCCCGTCGGCAACGGCAGAAATGCCCCGACCAGGTCCA\n+GCAACAGAAG\n'

diff -r 000000000000 -r d9f4c141d88a test-data/result2_scaffolds.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result2_scaffolds.fasta Tue Sep 25 05:24:27 2018 -0400

diff -r 000000000000 -r d9f4c141d88a test-data/result3_contigs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result3_contigs.fasta Tue Sep 25 05:24:27 2018 -0400

b'@@ -0,0 +1,548 @@\n+>contig_1\n+ATCGAAATCAGTCGATACCGCAGTGATATATCGTGAACATGGGTGCAACGCTGAGTTACA\n+GACATGCGCCTGGGGAACGGTAGGGAAATGAACCTGGCTGAAGGCGGCTGTGACGCAAAG\n+TAAATTTGTCGATGATAACCGGCCGGTGAAGGTGAATAATGACGCGTAATTTCGTCAATG\n+ATTTGTCGGCAGACGTGAATATACCAGGCAGCTATCTAAAGCCTCATTCAGCAGTACGTT\n+TAGCGACATCTCGCGGGTGGCGGTTATAGCCATGGTGCGGTGTGGAATCCCGCATGGAAC\n+GCGTGCGCTGGTGTGAACAATCGTGCGTTCTGACCATCAACGATATAAACTGCGCTCGGC\n+GCAGTTTTCCGTTTACAGATGTTGAATAGGGAAAATCTGGCGGCAAAAAAAGCCCGACCA\n+GTTACGGCGGGAAAACCTCATCCTATGGGAGAACAATGCAATAATGAAAATTGCGGGGTT\n+ATCATCTCCCAGTCATATCCAATACTAACAATAAGTTACTCTACTCAACGCAGCATAAAC\n+ATTTGTTTTGTGCGTGGGAACACGCCTTAAGGTGGTAAAGGGCGAGTGGAATAGCAAATG\n+AGCGAGTATCAGCAAGAATACTCCGCGCTTTACCACAACGTGATGAGAGCGCATGAAAAC\n+TGCAAGCGCAGAGATAACTCGCCTGCTTGAGATAAATGCGTGCTTTTATCAGCGGCTTTA\n+TTTTCAGCTCTTACTGCTTCCGTAGGTCACGTTCAGCTCAAGAATAGAGAAATATCGCCA\n+TCTTTTGCATCAAGCTGTACGTCTGTACCGATCTCAGCATCAATTTGCTACGTATTTACA\n+AATGACCTCAGAATATCCTTTACGCACTGCGGCAGATAATGCGGTTCTGCATCGCTGCGA\n+CGGCGTCAGCAAGCAATAATCTGCAGCCGTTCTTTTAGCAATGTTGCTGTGTTTTTCTTG\n+CGCTGCGAGAGAAGAAATCGAGTAATGACCATAACTTATGCCTCTCGAACAAGCGTTGAG\n+GAAGCCTTTCTTCTCCTCTTCAATGACCAGCGGAAAAGGACGTGGTCTTCTCCCAACAGA\n+CGTTCTACTACGGTATCTGCGTATGGCTTTACCGCAGCGCGTTAATGTCGAGAATGACCG\n+GTTTCACACCCTGGTTAGAGCGCGCGCAATACTGATTGATCCTCTGGGATGCACGCCGAC\n+GAGTTCTGATGCGCAGGATCTCACAGCACATGCTTCGCATGCTCAGCATGTCACCTCGGC\n+TTACGCGGCCTGCGGTTATAGCGCGTTAACAGCAGGTGCATCTTTAATAGGCTCTTCGCG\n+CCATTTTCTGCGCGGCGTGATTTCGACGCCAGAATGCCCTAAAATTACGTCAGAGTCGCG\n+TACTGAGGAGACTCCGGTGTTGGTGGTAATAATGCAGCTTCGTCTGCAAAATAGAGTGCG\n+CATTAACGCACCGGTTTAAACAATCCTGCGGGGAGGCACAAACGATAAATTCAAAATCCA\n+GCGCTTTCAGATCATCAAGAACTTTGCGACCCTTCACGGCTGAGGTCATCTTTATCGCGT\n+GTTTGCGACTGCCGGCAGAATATAGAGATATTTTCAGTACGCTTTATCTTTAATTAACGT\n+AACGCCTGATTTAGCGTTGCATCGCCTGAATGACGTTGACGAAATCTAGGTAAACGACCC\n+GGCGTCACAACCCATTAATCAGGTCGAGAGTACGCAGGCCGATATCAAAATACTATCACG\n+ACAGTTTTGCTTTCCTTCTGGGCCAAACCAGTGGCGATGCCGCGCTGGGAGGTGTCTTAC\n+CAAACACTTTGCCCGATAAGTAACAACAATAATGCGTGCCATAAGAATTCCTTGTTAAAA\n+AGCCGATCAATTTAACGGTTGTAACGGTCAATAAGCGTTTTCGACTAACTGCAGTCGCGC\n+CGCTTTGCCATAAAATTCTGCTGCGGATTTGATCACTCAGCCAGTATTCACCTGCGCATG\n+GACACCAGTTCCGCCATGCAGGTTCGTACAAAATATTTGCGTTTCCCGGTCACGCACTTG\n+CCCCTGCCAGCGCACGACCGCGCATTCATGCCATATGACATGAATGTTCCCATCGGCATC\n+AAGTTCGGCCCCAGCGCCTAACCGTGCTTGTAACAATCAGATCACATTGTGCCGAGCATT\n+AATACGCTGCACCGGACGCACCGCGGGTCGTATCTATTAAACGCGTTTTTGTGACCGCGT\n+TGTATTTTTGCGCTGCGGCAGCCTGCGGTGTGTTGGCGCTGGCAACGTGGCGCTTTTTCC\n+CCTTTCCTTCCGTCAGGCATAGGCAGCCCATCTTTTCAATTTCGCTTTAAGTTGCGCATC\n+TTTGCAGCCACTACGCCAATAACCGCGGCAACGCGTTGCCGAAACCGCCTGTATGCATCG\n+CTGACAGGTTTACCGGTCTTCCAGTGCCTGACGTTGAGTACAACGGGCATGTTTTAAAAA\n+TGGCGGGGCCTGAGCGATTTGTCTTCCAGCGCCTGATGGACTAACCTTAGGTTCTGCCTC\n+ATGCAGATCGAAAAGCCCACAGATAAAGGGAAGCTACTGCCTTTTTCAAGCTGCGATTGG\n+CGTGTTTGACATCCTGGCCTTATCGCAATTAGCTATTAATCATCGCCACGCGCGCGATGA\n+TGTGCCGACGACTATATAGGCATGTTATAGTCTGGATTATTTTGCAGGCAAGTCACCCTC\n+CCATTTATTCAGAGTAAAAGTCGTATCTGTGATAAATGGCGCTGATTCATAGCTTAAAAA\n+ATCCCTTGTCAATCAACCCATTGCCGTCGTACCGGTTTGATTGTTCTTATTTACGCTTCC\n+TTTTTCCGCACCCTAATCGTGCACAGCATCTCCAGACCTGTTTAAATATCCAGTATGGAG\n+GGGCAAGTGTTATCACCACGCCAGCGCTTTCTTACTTTCCATTTTTTGCGCATGCATTAA\n+AGAACACGATCGCTTATCTTAATATCCGCCACAGAATTGCTCTATCATAGCAAACCGCAG\n+AAGACGTCTGATACTTCGGTCAGCGTCATCGTAACTCGTCAGGTCAGCGGGTTTTGATTA\n+CGCGATTGATGATGACATGACGCATAAGTGTCTGTACGCGTTGGCATTATCAGGATGTGC\n+TATGAATATATGATGCGTATTTTTATATATCGGTATTGTCAGGTGACACTGTGGGATGCC\n+ATGTTCTCATCAATGGCGTCTGGGAAATGACGCTGGCGGACTTCAATCTCGGCGTGCGGC\n+GTTGTTTGCGACGCCGTATATTTGTGTGAACTCAGTATGGGCATTGCCCAGAGTTAACAA\n+GCGAAATATCTCGGCGAGAAAAGCCGCTGAAAACCTTACAATCATACCAGGCTACGATCC\n+CAGCGAATTTACATCGCTACCGGTGTATTTGCGATGTTAAAGAAAAATTATGTCGTGATG\n+ATCGTTATTTTGGGTGTGGATGGTAGCGGAGTGGAAAAATCAATCAAACCACCACAAAGA\n+TGTTATTTATGTGTCGTGAGTGATGTCTTGTTTACATTATGTTCTTATTCGTCATTAACC\n+TCTTGAGCGACAGAGAGGAGTGGGGCATTAACGTTTATGACGGGAGAGTCCCGTCGTTGA\n+CATTTACTTAATTTTGAATATCGACGTTTATATTTTTAGTTTTGTTTTTACGGGCGTCGT\n+TTCGGTTTGCAACACTCGCAGCTCATATTTGCCAGAAGCAGGGAGTGAGTATTGTCCCGT\n+GACTATCGAGTTCTGGGGAATATCTGGATAAATCAACTGGAATCATCGATTCTGGCCCGA\n+AGAGGTAAGTATCAGCGCCTTCATTAGAGATACTCTCACATGCACTTTCTGACCTTTTTG\n+G'..b'AAGCAACCTTTGAAAGCCAGCACCAG\n+TTTATTATGCGGTGATAACCCTTAAACCATAATAGAACGCAGGAACCAGCTTTATTTTGT\n+GTGCTCCCATCCTGTGGAACGAGATCGGCAGTGATGACCAGTCAATTAGGAAAAGTCAAA\n+GCCATACCTCGCTCATTATGCCACAGGACGATCCGCAAACCCGCCGCTTGATTTCATTTT\n+GTCGCCAGGCGTCGCGCAGAGCCTTTCCTGTCCTGCTTTTGTGGAGAAGATGGCGTGGCA\n+AGCACTGCCCTAAGTCAGGCAATTCATAATGAAAGCGAAGCTTGCTGCAGAGGTCCTTAT\n+AATCCCGTCAATTGGAGTTATTATTGTGAGCTGCGCTGCGAATTAATTTATGTGGCGATC\n+GCTACGGACAATGGAAAATGGCCGTCTTGAGTCGGCTGGAAACTGGCACCGGCGGCACGC\n+TGTTCTTGAAAAGATTGAATATCTGGCGTTGAGTTACAGTCTGCTTTGCTTCAGGTTATC\n+AAGCAAGGGGGTTATCACCGCGGACTGGTAATGCCGGCCGTTTTAATACCAATTGATGTC\n+AAAGTGAATTGCAACAACGAACCGCGGACCTCGCAATGCTGTGGCAACCAAAATCGTTTT\n+AGTCGCCACCTGTATTACGCGCTGCCATGCACTTTGAAATTACCATCCCGCCCTCTCGTA\n+TGCGGCGTGCAGCATTTCCGTGCGCTGGTGGAATAACAAATACGCAGGCTTGAAAAACGC\n+TTCTCTACGCGGCTCTGAAAATGATGACGTGCCCTCGCCTCGCCTGGTTTCTTGGCATGG\n+CCAGGCAACGATTTGAACTTTTACAGCTCATCGAGAATCTTGCTCTGAGTAGTGATAAAC\n+GGCGCAGTCCCGTCAGTAATTTGCCTGGAAACATCTGTTTACCGCAGGCAGGCGTGACAG\n+ATGATGTCAGCGCCACCCGCCCTTTCCACCAGTCTGTCATTTCGCGGAAGTTGAAAAAGA\n+GGAATTATAACGCAGCCCAGGTACAGGCCGGTCGCATTCAGGAAAGTCGCTTATTGATCG\n+CCCCGCCACTACGCTGTGGCGGAAAATGAAGGCAAACATGGCATTGATGCAGGGCAGTTA\n+AAGCGCCGGGTATTGAAAGACAGAAACGATTTCTGATACATCAGAGTGATCTGTATTTCA\n+TTCCGGCCACTGCTAACAATTTTCAGCATCGTTTTAAGCTTGTCTATCCCGCCACTTTAA\n+AAAGCTAAGCGATATCCTCCGTTGACTGCTCTGATTCAAAGAGGTTACCTCGGTAATCCG\n+CTTCGAGATAGAAATGATGTGCTTGTTTGTTATACTGGCATGGACTCCCATCGCGTTATT\n+CCAGCCCATTACCGAAAACCTGTACTTCTCCCGGGAGTTGTTCAAACAGATATTTCGGTA\n+TCCCCTGAAAACTCGCGTATAGCGCCAGTCTCACATAGACATTCAGCTGGCGTTGCCTGC\n+GTATGTCATCCCCAGTTATCATGCTGGCACGCCCCAGCCAGCGATTCGTTAGTGGATTCA\n+GCATGTATATTTGAAGGCCATTACTCCCCAATCATCTCATTCTGCGCTGGCGTATGTAAG\n+CTGGGTTTGCGGCTCTAATAGAACCCATAACCAGGTAGGGACAGGTTTGACCTCTTGCCC\n+GCTTCCAGGGAGATGCTCATTTCCCATTCGCAGTGCCGTTGCGTTAACTCCGTTTGTTCT\n+GACTGTCCAGTACGTGGAAAAAACTATTTTTCTGCCGCGATGCTTTATAACGAGACGCTG\n+TAAAAACCGTTTTGTGCCATGTAAACTGGCGAACATTCCCCATGTATCTGAACGTGCGGT\n+ACGTCGCCTCCGCTATGTCCGCGATGCATGTGTTGAGCCAAATATACAGACGACATACAA\n+ACGCATACATCAGAGAGACGTTATCCCCACCAAACTGTACCGCTGTAAACCACATGTCAA\n+AGCCGCCCTCAGTTTGCCACTGGCAAAGGAAGTCCAGGCTTCCCCATAAAGCGAACCAGA\n+TATTACGTCTTTACTCGATTGCGCAGGTCACCCATCCGTGCATCAGCGTACGGTTTTCAA\n+CATAGTCAATAAGTAACCACATTGAGATAATTGCCGCCAGCATCTGCGTCGTGGTGAGCG\n+TTTAGGCGTGAGCGTTCAGGCCGTAGATCGGGCGTTGGCTATGGAGCTGAGCGGGAGCTG\n+TGTGGTTTCAGATTAGAGTCGGTTCCGAACTTTCCCGGCAAGCGTAAAGCTCCCAGTTAG\n+TTCCATTTACGGGCACATCGTTACAAGATATCCCCCAACCAACCTGAGAAACGCGCTGAA\n+CGAGGCCGCCCGTCAGTGGTTTTTACCACTGTCAAACTTTCATTTCCCGTTGTCGCCTCG\n+CTGCCCTGGTTTCGGATAGCAATACGTGATTACCAGCACTACTCCCGCTGATATTCAATT\n+TAAATCCCCTTTATTATTTAACGCCATTACCCTCGCCACACATCAGCACGCATAATAAAT\n+GGTATGTTACGCGCATTCTCTACGTTATGTGCAAGTCCGCAGTTGACCGTGGCTGCAAAA\n+TCGACAGTGAATGCTCAGCGCCAGCGTGTCGAGATTAGAATTACTTGTTAACGTTCCGAC\n+GCTGTTATTCACGCAACGTCCAGTTTCCCCATTGGAACATTATCGCTGAAGGGAGGAACC\n+TGTCCAAAACCGACCCAGGGGGCATATCCAGATTGATTAGCCCACCTTTGGAAAGAACTG\n+CTACCTTGATAAGCATACGACCGAGTCGTGAGCGCTGCGGCATAACCATCGTCATGGTGC\n+GTTGCGATGCATCTGTCGGGTTACTCATATCAATGACCAGAATCGCTCGTGAGGTCGATC\n+TGGCTGTGGTCATGGCATAAATTTCCCCTGGCTCCTTGCCGCGCCGGTGATAGCCAACTG\n+TCTCCGGTTATCTACGCCGCTGAGAGCCCACCAAACCCAGCGCCAGACTGCCATTACGAT\n+CAACTGAATATCGGTATTTTGCATTTTGACAACAGCGTTGCCGTCTGGCCAGGCACCATA\n+AAGAAACCGCCGAAAAGATCTGATTTCGTTCGCGCCTGCAGAAATGATTATCGCGTCTGA\n+ACCACTGGTGACGAGGCCACCGCCCTGCGCGAAGAAATATGCTATCTGCACCGATAGTGT\n+TGTACCACCACGGAACTTCGACGCCATTGCCGCGGCTCCAGTTACATCAACAGTGAGTGC\n+ATTCGCGCCTAAACTGGCCAAACTCCAGAGGCCGTAGCATTATCGCATTGGTTTAAGTAC\n+TGTTTGTTCCGAGATCGACACAGATTTTTCTGTACGTTTTTCCCCATGCGCGTAGCCCTG\n+GAAATCGATTGTCAGTCTGTAGCCGTAAAACGCGCAGCACCAATTGTCGTTATTGCCGTG\n+AACAACCGATATAAACACCGTATTCCATCGTCGCGTGATTTTTACTTCCGCTTCCAAGAA\n+TCACACTGTTGCCATAGTCATTGATGGTTAGCCTTATAACCGTTCGATTTTCAATGGTGA\n+ATGAAGTGGCTGTTAGGTGAAAGCTATTTGCCCAATAATGATGCCGTCAATCGTTACTTC\n+TTAATGTGCTGGCTGTGCCTAAAGTCAGCATTGGTATAGTTCACCAATTAAAGTAATGCC\n+GAGGCAGGAGGTTGACCAACCAACAAATCTACTGTGAGTTCCGGTAAAGCTGTCAGGGAG\n+TTGTTTTTGCCCTGAATAATGAATTTTCCTTTTTGCATTAAATTTTTCCAAGAAAGCCCC\n+CGTCGTTGAAACATTGACGTGAACCCCAATTTCAATTTTAACCCCCAAGGTTTTGATATT\n+TTTGCCCCAGGGGCCCCGTTTGGTTTCCTTGCGGGGGCCATTTCGTGGCGTGTTCGTGTG\n+TG\n'

diff -r 000000000000 -r d9f4c141d88a test-data/result3_scaffolds.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/result3_scaffolds.fasta Tue Sep 25 05:24:27 2018 -0400