# HG changeset patch
# User iuc
# Date 1550510086 18000
# Node ID de387b2b28030cc65301d8228c13045c0e01f4e2
# Parent  98242353faa48e20859a16b8b8cd2a3e0d49a6f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit d44d890566efb82b4ce8a9ed2903b0902f3884ca

diff -r 98242353faa4 -r de387b2b2803 megahit_wrapper.xml
--- a/megahit_wrapper.xml	Mon May 14 06:11:34 2018 -0400
+++ b/megahit_wrapper.xml	Mon Feb 18 12:14:46 2019 -0500
@@ -1,8 +1,8 @@
 <?xml version='1.0' encoding='utf-8'?>
-<tool id="megahit" name="MEGAHIT" version="@VERSION@.3">
+<tool id="megahit" name="MEGAHIT" version="@VERSION@.4">
     <description>for metagenomics assembly</description>
     <macros>
-        <token name="@VERSION@">1.1.2</token>
+        <token name="@VERSION@">1.1.3</token>
     </macros>
     <requirements>
         <requirement type="package" version="@VERSION@">megahit</requirement>
@@ -22,15 +22,20 @@
             -1 '${input_option.batchmode.pair_input.forward}'
             -2 '${input_option.batchmode.pair_input.reverse}'
         #end if
+    #else if $input_option.choice == 'interleaved'
+        --12 '${input_option.interleaved_file}'
     #else
         -r '${input_option.single_files}'
     #end if
     ##basic assembly
     --min-count '${basic_section.min_count}'
-    --k-min '${basic_section.k_min}'
-    --k-max '${basic_section.k_max}'
-    --k-step '${basic_section.k_step}'
-    --min-contig-len '${basic_section.min_contig_len}'
+    #if $basic_section.k_mer.k_mer_method == "klist_method":
+        --k-list '${basic_section.k_mer.k_list}'
+    #else:
+        --k-step '${basic_section.k_mer.k_step}'
+        --k-min '${basic_section.k_mer.k_min}'
+        --k-max '${basic_section.k_mer.k_max}'
+    #end if
     ##advanced assembly
     ${advanced_section.nomercy}
     --bubble-level '${advanced_section.bubble_level}'
@@ -40,17 +45,22 @@
     --low-local-ratio '${advanced_section.low_local_ratio}'
     ${advanced_section.nolocal}
     ${advanced_section.kmin1pass}
+    --min-contig-len '${output_section.min_contig_len}'
 && cat megahit_out/log
     ]]></command>
     <inputs>
         <conditional name="input_option">
             <param name="choice" type="select" label="Select your input option">
                 <option value="single" selected="true">Single</option>
+                <option value="interleaved">Interleaved-paired-end</option>
                 <option value="paired">Paired-end</option>
                 <option value="paired_collection">Paired-end collection</option>
             </param>
             <when value="single">
-                <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" />
+                <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz,fastq.bz2" multiple="true" label="Single-end file(s)" help="Accepts fasta (.fasta, .fa) and fastq (.fastq) formats as well as gzip (.gz) and gzip2 (.bz2) files" />
+            </when>
+            <when value="interleaved">
+                <param name="interleaved_file" argument="--12" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz,fastq.bz2" multiple="true" label="Interleaved-paired-end file(s)" help="Accepts fasta (.fasta, .fa) and fastq (.fastq) formats as well as gzip (.gz) and gzip2 (.bz2) files" />
             </when>
             <when value="paired">
                 <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/>
@@ -72,14 +82,24 @@
             </when>
         </conditional>
         <section name="basic_section" title="Basic assembly options" expanded="True">
-            <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
-            <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
-            <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="255" help="must be odd number"/>
-            <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
-            <param name="k_step" argument="--k-step" type="integer" value="12" label="increment of kmer size of each iteration" max="28" help="must be even number"/>
+            <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers" help="(kmin+1)-mer with multiplicity lower than d (default 2, specified by --min-count option) will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly. If you want to use MEGAHIT to do generic assemblies, please change this value according to the sequencing depth. (recommend --min-count 3 for >40x)."/>
+            <conditional name="k_mer">
+                <param name="k_mer_method" type="select" label="K-mer specification method">
+                    <option value="klist_method">Specify list</option>
+                    <option value="klim_method">Specify min, max, and step values</option>
+                </param>
+                <when value="klist_method">
+                    <param name="k_list" argument="--k-list" type="text" value="21,29,39,59,79,99,119,141" label="comma-separated list of kmer size" help="all must be odd, in the range 15-255, and with increments &lt;= 28"/>
+                </when>
+                <when value="klim_method"> 
+                    <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size." max="255" help="Must be odd number. For ultra complex metagenomics data such as soil, a larger kmin, say 27, is recommended to reduce the complexity of the de Bruijn graph. Quality trimming is also recommended. For high-depth generic data, large --k-min (25 to 31) is recommended. Smaller --k-step, say 10, is more friendly to low-coverage datasets."/>
+                    <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
+                    <param name="k_step" argument="--k-step" type="integer" value="12" label="increment of kmer size of each iteration" max="28" help="must be even number"/>
+                </when>
+            </conditional>
         </section>
         <section name="advanced_section" title="Advanced assembly options" expanded="False">
-            <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue=""  label="do not add mercy kmers" />
+            <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue=""  label="do not add mercy kmers" help="Mercy kmers are specially designed for metagenomics assembly to recover low coverage sequences. For generic dataset >= 30x, MEGAHIT may generate better results with no mercy kmers." />
             <param name="bubble_level" argument="--bubble-level" type="integer" value="2" min="0" max="2" label="intensity of bubble merging (0-2), 0 to disable" />
             <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" />
             <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />
@@ -88,9 +108,17 @@
             <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
             <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" />
         </section>
+        <section name="output_section" title="Output options" expanded="True">
+            <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
+            <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>
+        </section>
     </inputs>
     <outputs>
         <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />
+        <collection name="intermediate_contigs" type="list" label="Intermediate contigs from ${tool.name} on ${on_string}">
+            <filter>output_section['show_intermediate_contigs']</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*\d)\.contigs\.fa$" ext="fasta" directory="megahit_out/intermediate_contigs" />
+        </collection>
     </outputs>
     <tests>
         <test>
@@ -105,6 +133,13 @@
             </output>
         </test>
         <test>
+             <conditional name="input_option">
+                <param name="choice" value="interleaved"/>
+                <param name="interleaved_file" value="interleaved-fq.fa"/>
+            </conditional>
+            <output name="output" file="interleaved_result.fa"/>
+        </test>
+        <test>
             <conditional name="input_option">
                 <param name="choice" value="paired"/>
                 <param name="fastq_input1" value="paired-fq1.fa"/>
@@ -113,23 +148,23 @@
             <output name="output" file="paired_result.fa"/>
         </test>
         <test>
-          <conditional name="input_option">
-            <param name="choice" value="paired_collection"/>
-            <conditional name="batchmode">
-              <param name="processmode" value="merge"/>
-              <param name="pair_input_list">
-                <collection type="list:paired">
-                <element name="Pair1">
-                  <collection type="paired">
-                    <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
-                    <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
-                  </collection>
-                </element>
-                </collection>
-              </param>
+            <conditional name="input_option">
+                <param name="choice" value="paired_collection"/>
+                <conditional name="batchmode">
+                    <param name="processmode" value="merge"/>
+                    <param name="pair_input_list">
+                        <collection type="list:paired">
+                        <element name="Pair1">
+                          <collection type="paired">
+                            <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
+                            <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
+                          </collection>
+                        </element>
+                        </collection>
+                    </param>
+                </conditional>
             </conditional>
-          </conditional>
-          <output name="output" file="paired_result.fa"/>
+            <output name="output" file="paired_result.fa"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -149,4 +184,4 @@
     <citations>
         <citation type="doi">10.1093/bioinformatics/btv033</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file
diff -r 98242353faa4 -r de387b2b2803 test-data/interleaved-fq.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interleaved-fq.fa	Mon Feb 18 12:14:46 2019 -0500
@@ -0,0 +1,400 @@
+>megahit_ref_example_454_1062_2:0:0_1:0:0_c8/1
+GTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTAT
+>megahit_ref_example_454_1062_2:0:0_1:0:0_c8/2
+CCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTAAGCCAATATCAGCGATGCCGAACGTATTTTTGCCG
+>megahit_ref_example_183_711_2:0:0_2:0:0_c9/1
+AACATCCATGAAACGCATTAGCACCACCATTACGACCACCAACACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCC
+>megahit_ref_example_183_711_2:0:0_2:0:0_c9/2
+ACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCGAACAAACTAATGGCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAA
+>megahit_ref_example_447_926_3:0:0_0:0:0_ca/1
+CTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCTGCCAGGATGCTTTACCCAATATCATCGATGCGGAACGTATT
+>megahit_ref_example_447_926_3:0:0_0:0:0_ca/2
+GCCACTGATGTACCGCCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGG
+>megahit_ref_example_35_557_3:0:0_4:0:0_cb/1
+TCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTTGTAACCAGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTT
+>megahit_ref_example_35_557_3:0:0_4:0:0_cb/2
+AGTTCGGCAAAAATACGTTCGGCATCGCAGATATTGGGTAACGCATGCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTAGGTGATTTTGG
+>megahit_ref_example_423_941_6:0:0_1:0:0_cc/1
+GCAGGGGCAGGAGGCGAGCGTCCTCTCTGCCCCCGCCAAAATCACCAAGCACCTGGTTGCGATGATTGAAAAACCCATTAGCGGCCAGGATGCTTTACCC
+>megahit_ref_example_423_941_6:0:0_1:0:0_cc/2
+AAACGTTCTGCATTTGCCACTGATGTACCGCCGGTGAAAGCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACT
+>megahit_ref_example_683_1208_1:0:0_1:0:0_cd/1
+TGGAACTGGGCGATGGGGGTAATGGTGCGGGGGTGAAGAACATTAGCGCCGAAGTAGGAAAGCTCCATCGCTTCCTGGTAGGACATCGACTTCAACAACC
+>megahit_ref_example_683_1208_1:0:0_1:0:0_cd/2
+ATAGCCTCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGA
+>megahit_ref_example_102_568_2:0:0_1:0:0_ce/1
+GTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCAAATGGTTTTTTCAATCATCGCCACCAGGTGGTT
+>megahit_ref_example_102_568_2:0:0_1:0:0_ce/2
+AAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGCGTACACAACATCCATGACACGCATT
+>megahit_ref_example_435_844_3:0:0_2:0:0_cf/1
+ACTCAGCAATCTCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATACCAGTAACGTTGTGACCGCGCGCTTCTAATAC
+>megahit_ref_example_435_844_3:0:0_2:0:0_cf/2
+GGCCACCGTCCTCTCTGCCCCCGCCACAATCACCACCCACCTGGTGGCGATGATTGCAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGAT
+>megahit_ref_example_551_990_1:0:0_2:0:0_d0/1
+CCGAACTTTTGAGGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCT
+>megahit_ref_example_551_990_1:0:0_2:0:0_d0/2
+GCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCCGAAAACGTTCTGCATTTGCCACTGATGTCCCGCCGGTGAAACCTGCCATCAGC
+>megahit_ref_example_446_903_2:0:0_2:0:0_d1/1
+ACCTGCCATCAGCACCATGTGATCAGCCGGAAAGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTACTGCCCCACT
+>megahit_ref_example_446_903_2:0:0_2:0:0_d1/2
+TCTCTGCCCCCGCCAAAATCACCAACCACCAGGTGGCGATGATTGAACAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTAT
+>megahit_ref_example_274_766_8:0:0_1:0:0_d2/1
+TGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCCA
+>megahit_ref_example_274_766_8:0:0_1:0:0_d2/2
+AAAAAATCCCGCACCTTACAGTGCGGGCTTTTTTTTTCGACCAACGGTAACGCGGAAACAAGCAAGCGAGTTTTGAAGTTCGGCGGTACATCAGTGGCAA
+>megahit_ref_example_302_779_3:0:0_4:0:0_d3/1
+TATTTTTTTCGACCAAAGGTAACGAGGTAAGAACCATGCGAGTGTTGAAGTTCGGCGGTACCTCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGA
+>megahit_ref_example_302_779_3:0:0_4:0:0_d3/2
+ATAACCGTACCGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGGCACGGCAAATCAGCGCAGCGTTGATTCTATCCG
+>megahit_ref_example_664_1070_2:0:0_5:0:0_d4/1
+CCGTCACCGTCCGTCCAAATCTCGCAACAAACGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCTTTGCGTCCAAGGACCCCCAGTT
+>megahit_ref_example_664_1070_2:0:0_5:0:0_d4/2
+TTGTTGGGGCAGTTCCCGGATAGCATCAACGCTGCGCTGATTTTCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTC
+>megahit_ref_example_190_676_5:0:0_0:0:0_d5/1
+ATGAAACGCATTAGCACCACCATAACCCCCACCAACACGATTACCAGAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCT
+>megahit_ref_example_190_676_5:0:0_0:0:0_d5/2
+ACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGC
+>megahit_ref_example_105_589_1:0:0_3:0:0_d6/1
+ACCCCGGCTGGTCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGTTAAAGCATCCTGGCCTCTAATGGTTTTTTC
+>megahit_ref_example_105_589_1:0:0_3:0:0_d6/2
+ATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGCTAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGC
+>megahit_ref_example_67_585_6:0:0_2:0:0_d7/1
+CGGCTGGGCGGCGGCGAGTCCCGTCAAAAGATCGGCAAAAATACGTTGGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATC
+>megahit_ref_example_67_585_6:0:0_2:0:0_d7/2
+CAGCTTCTGAACAGGTTACCTGCGGTGAGTAAATTAAAATTTTATTGACTTCGGTCCCTACATACTTTAACCAATATAGGCATCGCGCACAGACAGATAA
+>megahit_ref_example_227_810_3:0:0_2:0:0_d8/1
+CCCCACTGCCAGCCGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCC
+>megahit_ref_example_227_810_3:0:0_2:0:0_d8/2
+CCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAACAAAGCCCGCACCTGCCAGTGCGGGCTTTTTTTTTCTACCAAAGGTAACGA
+>megahit_ref_example_18_544_4:0:0_3:0:0_d9/1
+GCAACGGGCAATATGTCTCTGTGTGGATTCAAAACAGAGTGTCTGATAGCAGCATCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTTACTT
+>megahit_ref_example_18_544_4:0:0_3:0:0_d9/2
+TACGTTCGGCCTCGCTGATATAGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGTCGGGGGCAGAGAG
+>megahit_ref_example_156_643_1:0:0_1:0:0_da/1
+GTTTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTGAAAAGTTCGGCAAAAAT
+>megahit_ref_example_156_643_1:0:0_1:0:0_da/2
+CAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGTTAACGGTGCGGGCTGA
+>megahit_ref_example_33_483_0:0:0_2:0:0_db/1
+TCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACT
+>megahit_ref_example_33_483_0:0:0_2:0:0_db/2
+CGCCACCATGTGGTTGGTGATTTTGGCGTGGGCAGAGAGGACGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAA
+>megahit_ref_example_435_930_1:0:0_1:0:0_dc/1
+GGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGGGGCCAGGATGCTTTACCCAATATCAGCGAT
+>megahit_ref_example_435_930_1:0:0_1:0:0_dc/2
+ATTTGCCACTGATGTACCGCCGGTGAACCCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCG
+>megahit_ref_example_177_730_0:0:0_5:0:0_dd/1
+CGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGGGTTGATGGAATCCGGGCACTGCCCCAAGAAACTAATGCCCTGCAGGACATGTTTTATTTGGGC
+>megahit_ref_example_177_730_0:0:0_5:0:0_dd/2
+GTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAA
+>megahit_ref_example_298_798_2:0:0_4:0:0_de/1
+GGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCAGCGTGATG
+>megahit_ref_example_298_798_2:0:0_4:0:0_de/2
+CAGTTTTACGACCGGCTCGATAACAGTAAGGTTGTGACCGCGCGCTACTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGC
+>megahit_ref_example_14_510_4:0:0_3:0:0_df/1
+GACTGCAACGGGCAATCTGTCTCTGTGTGGATTAAAAAAAGAGTGACTGATAGCCTCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTG
+>megahit_ref_example_14_510_4:0:0_3:0:0_df/2
+CTGGCGGCTAATGGTTTTATCAATCATCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAGAGAGGCCGGTGGCCACCTGCCCCTGCCTGGCATTGCTT
+>megahit_ref_example_583_1052_1:0:0_2:0:0_e0/1
+ATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTCGTCGGAACCGTTGCGTCCAAGCACCACGAGTTCGCCTTTTTCATTACCGG
+>megahit_ref_example_583_1052_1:0:0_2:0:0_e0/2
+CCGGGTTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGG
+>megahit_ref_example_756_1204_2:0:0_2:0:0_e1/1
+ACTGGGCGATGGGGGTAATGGTGCGGGGGTGAAGAACTTAAGCGCCGAAGTAGGAAAGCTCCATCGCTTCCTTGTAGGACATCGACTTCAACAACCTCGC
+>megahit_ref_example_756_1204_2:0:0_2:0:0_e1/2
+GCGCGGTCCCAACTTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGT
+>megahit_ref_example_562_1125_5:0:0_2:0:0_e2/1
+ACGGGACTCGGCGCCGCCCAGCGGGTGAACCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTA
+>megahit_ref_example_562_1125_5:0:0_2:0:0_e2/2
+CATCGACTTCAACAACCTCGCATCGGGCACCTGACGCGGGTCGCAGGTATCGACCCCGTCAACGTCCGTCCAAATCTCGCACCAATCGGCGCGTAAACAG
+>megahit_ref_example_120_658_2:0:0_2:0:0_e3/1
+TGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAACGTTTTCAAATGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAA
+>megahit_ref_example_120_658_2:0:0_2:0:0_e3/2
+GTCACTACATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACCCAACATCCATGAAACGCATTAGCACCACCATTACCACC
+>megahit_ref_example_373_877_2:0:0_2:0:0_e4/1
+CCGGAATGCTGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGTTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGAT
+>megahit_ref_example_373_877_2:0:0_2:0:0_e4/2
+AATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCCGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACG
+>megahit_ref_example_266_798_1:0:0_4:0:0_e5/1
+AAACACAGAAAACAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATC
+>megahit_ref_example_266_798_1:0:0_4:0:0_e5/2
+CAGTTTTTCGAGCGGATCGATAACAGTAACGTTGTTACCGCGCGCTTCTAATACGCCGGCCATAAAGGGGATCGACATTTTCTCGCCACGGCAAATCAGC
+>megahit_ref_example_712_1227_3:0:0_3:0:0_e6/1
+TTTAATCAGGCAAGGGATCTGGAACTGGGCGAAGGGGGTAATGGTGCGGGGGTGAAGAACTTTAGCGCCGAAGTAGGAAAGCTCGATCGCTTCGTGGTAG
+>megahit_ref_example_712_1227_3:0:0_3:0:0_e6/2
+GGGGAGAAAATGTCGATCGCCATTATGGCCGGCGTAATAGAAGCGCGCGGTCAGAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGC
+>megahit_ref_example_324_891_2:0:0_3:0:0_e7/1
+CACCATGTGATCAGCCTGAATGCGGCTTGCCGCAATACGGCGGGTGGACTGAGCAATAACGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTT
+>megahit_ref_example_324_891_2:0:0_3:0:0_e7/2
+CGAGGTCACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGAGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGG
+>megahit_ref_example_579_1136_4:0:0_5:0:0_e8/1
+CCAGCCGTGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGAACAGGAATTTGCGCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGAGC
+>megahit_ref_example_579_1136_4:0:0_5:0:0_e8/2
+TCCTGGTAGGACATCGACTTCAACAACCTCGCATCGGGCACGTGACGCGGGTCGCAGGTATCGACCGCGTCAACGTCCGTCCAAATCTCGCCACAATCGT
+>megahit_ref_example_602_1113_3:0:0_2:0:0_e9/1
+CAACCTCGCATCGGGCACCTGACGCGGGTCGCAGGTATAGACCCCGTCAACGTCCGTCCAAATCTCGCAACACTCGGCGCGTAAACCGGCAGCCAGCACC
+>megahit_ref_example_602_1113_3:0:0_2:0:0_e9/2
+ACTTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCAGCATGGCAATAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCT
+>megahit_ref_example_623_1060_1:0:0_3:0:0_ea/1
+CCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGTAACCGTTGCGTCCACGCACGACCAGTTCGCCTTTTTC
+>megahit_ref_example_623_1060_1:0:0_3:0:0_ea/2
+AGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGGATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAAT
+>megahit_ref_example_574_1043_3:0:0_2:0:0_eb/1
+CAATGGGCGCGAAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCA
+>megahit_ref_example_574_1043_3:0:0_2:0:0_eb/2
+GCCGCGCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTAGCCCAAATAAAACATGTCCTGCATGGCATTATTTTGTTGGGGC
+>megahit_ref_example_524_1109_2:0:0_2:0:0_ec/1
+ATATCAGCGATGCCGAACGAATTTTTGCCGAACTTTTGACGGGACACGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCA
+>megahit_ref_example_524_1109_2:0:0_2:0:0_ec/2
+CTCGCATCGGGCACCTGACGCGGGTCGCATGTATAGACCCCGTCAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGGAGCCAGCACCGCAG
+>megahit_ref_example_181_689_0:0:0_2:0:0_ed/1
+ATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTTGGCCAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGA
+>megahit_ref_example_181_689_0:0:0_2:0:0_ed/2
+ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
+>megahit_ref_example_434_971_1:0:0_2:0:0_ee/1
+TGGCCACCGTCCTCTCTGCCCCCGCCAAAAACACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGA
+>megahit_ref_example_434_971_1:0:0_2:0:0_ee/2
+TCGCCTTTTTCATTACCGGCAACCCGCAGAAAACGTTCTGCATTTGCCACTGAAGTACCGCCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGGAA
+>megahit_ref_example_129_569_3:0:0_0:0:0_ef/1
+AGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGTGGT
+>megahit_ref_example_129_569_3:0:0_0:0:0_ef/2
+TACTTTAACCAATATAGGCATCGCGCACAGCCAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCCTCACC
+>megahit_ref_example_590_1073_0:0:0_2:0:0_f0/1
+ACCCCGTCAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCGAGCACCGCAGCAGAGTAGTCGGAACCGTTGCTTCCAAGCACCACCA
+>megahit_ref_example_590_1073_0:0:0_2:0:0_f0/2
+TCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCAT
+>megahit_ref_example_47_580_0:0:0_1:0:0_f1/1
+GGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTCAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGC
+>megahit_ref_example_47_580_0:0:0_1:0:0_f1/2
+AAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGG
+>megahit_ref_example_13_463_3:0:0_4:0:0_f2/1
+TTTTGGCGTGGGCAGAGAGGACTGTGGCCACCTGCCCCTGCCTTGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCAGTGA
+>megahit_ref_example_13_463_3:0:0_4:0:0_f2/2
+TGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAAGTGGTTAGCTGCCGTTAGTAAATTAAAATTTTATT
+>megahit_ref_example_84_599_1:0:0_3:0:0_f3/1
+GCCAGCGGGAAGCCCGGCTGGGCGGCTGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATCTTGGGTAAAGCATCCTGGCCGCTAA
+>megahit_ref_example_84_599_1:0:0_3:0:0_f3/2
+ACGTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACA
+>megahit_ref_example_155_674_5:0:0_1:0:0_f4/1
+ACAGAGAGAAAAAACTTACAGAGTACACAACATGCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCTGGCTG
+>megahit_ref_example_155_674_5:0:0_1:0:0_f4/2
+TGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGCTCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGG
+>megahit_ref_example_441_939_2:0:0_2:0:0_f5/1
+CGTCCTCTCTGCCCCCGCCAAAATCACCAACGACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATGAGCGATGCCGAA
+>megahit_ref_example_441_939_2:0:0_2:0:0_f5/2
+ACGTTCTGCATTTGCCACTGATGTACCGCCGGTTAAACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTGA
+>megahit_ref_example_205_721_2:0:0_2:0:0_f6/1
+ACCACCATTACCCCCACCATCACCATTACCACAGGTAACGGTGCTGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTT
+>megahit_ref_example_205_721_2:0:0_2:0:0_f6/2
+TTTTCTCGCCACGGCAAATCAGCGCAGCGATGATGGTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTG
+>megahit_ref_example_626_1145_0:0:0_1:0:0_f7/1
+AATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTC
+>megahit_ref_example_626_1145_0:0:0_1:0:0_f7/2
+TCCATCGCTTCCTGGTAGGACATCGACTTCAACAACCTCGCATCGGGCACCTGACGCGGGTCTCAGGTATAGACCCCGTCAACGTCCGTCCAAATCTCGC
+>megahit_ref_example_158_653_2:0:0_3:0:0_f8/1
+GACAGATAAAAATTACAGAGTACACAACATCGATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCAGACG
+>megahit_ref_example_158_653_2:0:0_3:0:0_f8/2
+TGCAGGACATGTTTAATTTGGGCAAATTCCTGAACGACGAAAGTTTTCAATTGCGCCAGCGGGAAGCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTT
+>megahit_ref_example_441_980_2:0:0_2:0:0_f9/1
+CGTCCTGTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTATACCCAATATCAGCGATGCCGAA
+>megahit_ref_example_441_980_2:0:0_2:0:0_f9/2
+ACCACCAGTTCGCCTATTTCATTACCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGGTGAAACCTGCGATCAGCACCATGTGAT
+>megahit_ref_example_523_1016_3:0:0_1:0:0_fa/1
+ACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCAGAAAACGTTCTGCAATTGCCACTGATG
+>megahit_ref_example_523_1016_3:0:0_1:0:0_fa/2
+CATATCAGCGATGCCGAACGTATTTTTTCCGAACTTTTGACTGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATC
+>megahit_ref_example_609_1083_1:0:0_1:0:0_fb/1
+AACTTTCGTCGATCAGGACTTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGC
+>megahit_ref_example_609_1083_1:0:0_1:0:0_fb/2
+GCAGGTATAGACCCCGTCAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGGAGAGTAGTCGGAACCGTTGCGTCCA
+>megahit_ref_example_189_694_1:0:0_1:0:0_fc/1
+CATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAAGACAGAAAAAAGCCCGCACC
+>megahit_ref_example_189_694_1:0:0_1:0:0_fc/2
+CGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCCATTGCGCCAG
+>megahit_ref_example_388_886_2:0:0_5:0:0_fd/1
+CTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTTGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTTGCGATGA
+>megahit_ref_example_388_886_2:0:0_5:0:0_fd/2
+TTTGATCATCCGGAATGCGGCTTGCGGCAATACGGCGGGTGGCCTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCATTTTTTCGAC
+>megahit_ref_example_283_879_1:0:0_2:0:0_fe/1
+CGCCCCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAAC
+>megahit_ref_example_283_879_1:0:0_2:0:0_fe/2
+AGCCGGAATGCGGCTTGCCGCAATCCGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGCCCGGATCG
+>megahit_ref_example_265_722_0:0:0_2:0:0_ff/1
+GAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACAT
+>megahit_ref_example_265_722_0:0:0_2:0:0_ff/2
+ATTTTCTCGCCACGGCCAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATTTTTTATTTGGGCAAATTCCT
+>megahit_ref_example_73_583_4:0:0_5:0:0_100/1
+CTGAACTGGTTACCAGCCGTGAGTAAATTAAAATTTTAATGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGGCCAGACAGATAAAAATTA
+>megahit_ref_example_73_583_4:0:0_5:0:0_100/2
+GCTGGGCGGCGGCTAGTCCCGTCAAAAGTTCTGCAAAAATACGTACGGCATCGCTGATATTGGGTAAAGCATCCTTGCCGCTAATGGTTTTATCAATCAT
+>megahit_ref_example_272_690_2:0:0_3:0:0_101/1
+AGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACCAGCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGC
+>megahit_ref_example_272_690_2:0:0_3:0:0_101/2
+GATGCTATCCGGGCACTGCGCCAACAAACTAATGCCATGCAGTACATGTTTTATTTGGGCAAATTCCTGATCGACGAAAGTATTCAATTGCGCCAGCGGG
+>megahit_ref_example_508_1069_3:0:0_1:0:0_102/1
+CATGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACTGGACTCGCCGCCGCCCAGCCTGGGTTCCCGCTGGCGCAATTGA
+>megahit_ref_example_508_1069_3:0:0_1:0:0_102/2
+CGTCAACGTCCGTCCAAATCTGGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTC
+>megahit_ref_example_25_484_4:0:0_1:0:0_103/1
+GCAATATGTCTCTGTGTGGATAAAAAAAATAGTTTCTGATCGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCAC
+>megahit_ref_example_25_484_4:0:0_1:0:0_103/2
+TCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAGAGAGGACGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGGAACACGCAGAAA
+>megahit_ref_example_349_870_2:0:0_2:0:0_104/1
+GGTGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTA
+>megahit_ref_example_349_870_2:0:0_2:0:0_104/2
+AAGTTCGGCGGTACCTCAGTGGCAAATGCAGAACGTTATCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCT
+>megahit_ref_example_333_946_2:0:0_0:0:0_105/1
+GCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGT
+>megahit_ref_example_333_946_2:0:0_0:0:0_105/2
+AACCATGCGAGTGTTTAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGGAGGGGCAG
+>megahit_ref_example_185_727_1:0:0_1:0:0_106/1
+CATCGATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCG
+>megahit_ref_example_185_727_1:0:0_1:0:0_106/2
+TCGACATTTTCTCGCCACGGGAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAA
+>megahit_ref_example_564_1103_0:0:0_1:0:0_107/1
+TCGGGCACCTGACGCGGGTCGCAGGTATAGACCCCGTCAACGTCCGTCCAAATCTCGCAACAATCGGCTCGTAAACAGGCAGCCAGCACCGCAGCAGAGT
+>megahit_ref_example_564_1103_0:0:0_1:0:0_107/2
+GGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGT
+>megahit_ref_example_511_952_2:0:0_3:0:0_108/1
+GATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCGGAACTTTTGACGGGAGTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAA
+>megahit_ref_example_511_952_2:0:0_3:0:0_108/2
+CAACCCGCAGAAAACGTTCTGGATTTGCGACTGATGTACCGCCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACG
+>megahit_ref_example_506_976_3:0:0_0:0:0_109/1
+CCAGTTCGCCTTTTTCATTACCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACCGCCGGTGAAACCTGCCATCAGCACCATGTGATCAGC
+>megahit_ref_example_506_976_3:0:0_0:0:0_109/2
+GCCATGATGCTTTACCCAATATCAGCGATGCCGAACGTAATTTTGCCGAACTTTTTACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATT
+>megahit_ref_example_512_1044_0:0:0_4:0:0_10a/1
+ACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCCCCAGTTCGCCTTTAACATTACCGGCACCACGC
+>megahit_ref_example_512_1044_0:0:0_4:0:0_10a/2
+ATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAAC
+>megahit_ref_example_194_708_4:0:0_1:0:0_10b/1
+AACGCATTAGCACCACCATTACCCCCACCCTCACCATTACCACCGGTAACGGTGCGGGCTGACGCGTACAGGAAACACATAAAAAAGCCCGCACCTGACA
+>megahit_ref_example_194_708_4:0:0_1:0:0_10b/2
+GCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACATGTTTTATTTGGGCAAAATCCTGATCGACGAAAGTT
+>megahit_ref_example_70_621_2:0:0_0:0:0_10c/1
+CTACTGAACTGGTTACCTGCCGTGAGTAAATTAAACTTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAA
+>megahit_ref_example_70_621_2:0:0_0:0:0_10c/2
+ATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTG
+>megahit_ref_example_220_627_1:0:0_5:0:0_10d/1
+ACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGGCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAG
+>megahit_ref_example_220_627_1:0:0_5:0:0_10d/2
+TTCCTGATCGACGAAAGTTTTCAATTGGGCCAGCGGGAACCGCTGCTGGGCGGCGGCGAGTCCCTTCAAAAGTTCGGCAACAATACGTTCGGCATCGCTG
+>megahit_ref_example_59_625_2:0:0_4:0:0_10e/1
+CCTGATCGACGAAAGTTTTCAATTGCGCCAGCGTTAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCACAACTACGTTCGGCATCGCTGAT
+>megahit_ref_example_59_625_2:0:0_4:0:0_10e/2
+TCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACAAAATACTTTACCCAATATAGGCATAGCGCACAG
+>megahit_ref_example_591_1209_1:0:0_2:0:0_10f/1
+CTGGAACTGGGCGATGGGGGTAATGGTGCGGGGGTGAAGAACTTTAGCGCCGAAGTAGGAAAGCTCCATCGCTTCCTGGTAGTACATCGACTTGAACAAC
+>megahit_ref_example_591_1209_1:0:0_2:0:0_10f/2
+CCCGCAGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATC
+>megahit_ref_example_80_615_3:0:0_2:0:0_110/1
+GAAAGTTTTCAATTGCGCCAGCGGGACCCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACGTTCGGCATCGCTGATATTGGGTCAA
+>megahit_ref_example_80_615_3:0:0_2:0:0_110/2
+GGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATCCTTTAACCAATATAGGCATAGCGCACAGACAGATCCAAATTACAGAGTA
+>megahit_ref_example_211_659_3:0:0_4:0:0_111/1
+ATTACCACCCCCATCACCATTACGACAGGTCACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTT
+>megahit_ref_example_211_659_3:0:0_4:0:0_111/2
+ATGCCCTGCAGGACATGATTTATTTGGGCAAATTCCTGAACGACGAAAGTTTTCAATTGCGCGAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCA
+>megahit_ref_example_396_888_1:0:0_1:0:0_112/1
+TGCCGATATTCTGGAAAGCAAAGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAA
+>megahit_ref_example_396_888_1:0:0_1:0:0_112/2
+CATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGCTTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCG
+>megahit_ref_example_469_944_3:0:0_3:0:0_113/1
+AGAAAACGATCTGCATTTGCCACTGATGTAGCGCCGGTGAAACCTGCCATCAGCACCATGTGATCAGCCTGAATGCGGCTTGCCGCAATACGGCGGGTGG
+>megahit_ref_example_469_944_3:0:0_3:0:0_113/2
+AACCACCAGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGCACGTATTTTTGCCGAACTTTTGACGTGAC
+>megahit_ref_example_469_939_2:0:0_3:0:0_114/1
+ACGTTCTGCATTTGCCACTGATGTACGGCCGGTGAAACCTTCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCC
+>megahit_ref_example_469_939_2:0:0_3:0:0_114/2
+AACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCCATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTAGACGGGAC
+>megahit_ref_example_502_1072_2:0:0_2:0:0_115/1
+CCCCGTCAACGTCCGTCCAAATCTCGCAAGAATCGTCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAG
+>megahit_ref_example_502_1072_2:0:0_2:0:0_115/2
+AGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCTCCGCCGCCCAGCCGGGGTTCCCGGTGGCGC
+>megahit_ref_example_3_472_1:0:0_0:0:0_116/1
+GGTTGGTGATTTTGGCGGGGGCAGAGAGGACGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATT
+>megahit_ref_example_3_472_1:0:0_0:0:0_116/2
+CTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAACGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTA
+>megahit_ref_example_578_1031_2:0:0_2:0:0_117/1
+AAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCCCCACCAGTTCGCCTTTTTCATTACCGGCAACACGCAGAAAACTTTCTG
+>megahit_ref_example_578_1031_2:0:0_2:0:0_117/2
+CCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTGGTCGATGAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTG
+>megahit_ref_example_131_641_1:0:0_4:0:0_118/1
+TTTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCATCGGGAACCCCGGCTGGGGGGCGGCGAGTCCCGACAAAAGTTGGGCAAAAATAC
+>megahit_ref_example_131_641_1:0:0_4:0:0_118/2
+CTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGCGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCAT
+>megahit_ref_example_484_1059_2:0:0_5:0:0_119/1
+CGACCAAATCTCTCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTATTCGGAACGGTTGCGTCCAAGCACCACCAGTTCTCCTTTTTCA
+>megahit_ref_example_484_1059_2:0:0_5:0:0_119/2
+ATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGACCGTATTTTTGCCGAACTTTAGACGGGACTCGCCGCCGCCCAGC
+>megahit_ref_example_296_795_0:0:0_1:0:0_11a/1
+TTTTTCGACCGGATCGATAACAGTAACGTTGTGACGGCGCGCTTCTAATACGCCGGCCATAATGGCGATCGACATTTTCTCGCCACGGCAAATCAGCGCA
+>megahit_ref_example_296_795_0:0:0_1:0:0_11a/2
+GCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGT
+>megahit_ref_example_557_1066_2:0:0_0:0:0_11b/1
+TTTTGACGGGACTCGGCGCCGCCCATCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGG
+>megahit_ref_example_557_1066_2:0:0_0:0:0_11b/2
+CAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCC
+>megahit_ref_example_177_758_0:0:0_2:0:0_11c/1
+GTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAA
+>megahit_ref_example_177_758_0:0:0_2:0:0_11c/2
+CGCGCTTCTAATACGCCGGCCATAATGGCGAACGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCGCAACAAACTAA
+>megahit_ref_example_108_607_3:0:0_2:0:0_11d/1
+TCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCTTCAAAAGTTCGGCACAAATACGTTCGGCATCGCTGATATTGGGTAAAGCATCCTG
+>megahit_ref_example_108_607_3:0:0_2:0:0_11d/2
+TTATTGACTTAGGTCACTAAAACCTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCCTTAGCACC
+>megahit_ref_example_590_1105_3:0:0_3:0:0_11e/1
+CATCGGGCACCTGACGCGGGTCGCAGGTATAGACCCCGTCAACGTCCGTCCAAATCTCGCAACACTCGGGGCGAAAACAGGCAGCCAGCACCGCAGCAGA
+>megahit_ref_example_590_1105_3:0:0_3:0:0_11e/2
+TCCCGCTGGCGCAATTGAAAACTTTCTTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATAAGATTGTTGGGGCAGTGCCCGGATAGCAT
+>megahit_ref_example_175_730_3:0:0_2:0:0_11f/1
+GAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCAGCATTACGACAGGTAACGGTGCGGGCTGACGCTTACAGGAAACACAGA
+>megahit_ref_example_175_730_3:0:0_2:0:0_11f/2
+CGATCGACATTTTCTCGCCACGGCAAATCAGCGCAGCGTTGATGCTATCGGGGCACTGCCCCAACAAACTAATTCCATGCAGGACATGTTTTATTTGGGC
+>megahit_ref_example_694_1127_1:0:0_1:0:0_120/1
+GCTGCGCTTATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAA
+>megahit_ref_example_694_1127_1:0:0_1:0:0_120/2
+GACATCGACTTCAACAACCTCGCATCGGGCACCTGACGCGGGTCGCAGGTATAGACCCGGTCAACGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAAC
+>megahit_ref_example_539_991_1:0:0_3:0:0_121/1
+TGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATTTACCGCCGGATAAACCTGCCATCAG
+>megahit_ref_example_539_991_1:0:0_3:0:0_121/2
+AACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGTGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAAT
+>megahit_ref_example_689_1161_1:0:0_0:0:0_122/1
+GCCGAAGTAGGAAAGCTCCATCGCTTCCTGGTAGGACATCGACTTCAACAACCTCGCATCGGGCACCTGACGCGGGTCGCAGGTATAGACCCCGTCAACG
+>megahit_ref_example_689_1161_1:0:0_0:0:0_122/2
+TCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTAGTGTTATCGATCCGGT
+>megahit_ref_example_371_878_3:0:0_1:0:0_123/1
+CAAATGCAGAACTTTTTCAGCGTGTTGCCGATATACTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAA
+>megahit_ref_example_371_878_3:0:0_1:0:0_123/2
+GCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTATTTCGACCGGATCGA
+>megahit_ref_example_407_902_2:0:0_2:0:0_124/1
+CCTGCCATCAGCACCATGTGATCAGCCGGAATGCGGCTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTCGATTCGATGTAATGCCCCACTG
+>megahit_ref_example_407_902_2:0:0_2:0:0_124/2
+TGGAAAGCAATTCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACGAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGG
+>megahit_ref_example_496_1063_2:0:0_1:0:0_125/1
+ACCATTAGCGGCCAGGATGCTTTACCCCATATCAGCGATGCCGAACGAATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGC
+>megahit_ref_example_496_1063_2:0:0_1:0:0_125/2
+CGTCCGTCCAAATCTCGCAACAATCGGCGCGTAAACAGGCAGCCAGCACCGCAGCAGAGAAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTT
+>megahit_ref_example_529_1002_0:0:0_1:0:0_126/1
+GTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCAACACGCAGAAAACGTTCTGCATTTGCCACTGATGTACGGCCGGTGAAA
+>megahit_ref_example_529_1002_0:0:0_1:0:0_126/2
+AGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAAT
+>megahit_ref_example_486_996_1:0:0_5:0:0_127/1
+ACCGTTGCGTCCAAGCAGCACCAGTTCGCCTTTTTCATAACCGGCAACACGCAGAAAACTTTCTGCATTTGCGACTGATTTACCGCCGGTGAAACCTGCC
+>megahit_ref_example_486_996_1:0:0_5:0:0_127/2
+GATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGAATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCG
+>megahit_ref_example_200_640_1:0:0_0:0:0_128/1
+TTATTTGGGCAAATTCCTGATCGACGAAAGTTTTCAATTGCGCCAGCGGGAACCCCGGCTGGGCGGCGGCGAGTCCCGTCAAAAGTTCGGCAAAAATACG
+>megahit_ref_example_200_640_1:0:0_0:0:0_128/2
+TTAGCCCCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGG
+>megahit_ref_example_370_888_2:0:0_2:0:0_129/1
+GGAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGGAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCA
+>megahit_ref_example_370_888_2:0:0_2:0:0_129/2
+CATGTGATCATCCGGAATGCGGCTTGCCGCAATACGGGGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCG
+>megahit_ref_example_335_841_1:0:0_2:0:0_12a/1
+CCATGCGATTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGT
+>megahit_ref_example_335_841_1:0:0_2:0:0_12a/2
+CAGCAATATCGACGGTAGATTGGAGGTAATGCCGCACTGCCAGCAGTTTTTCGACCGGATCGATAACAGTAACGTTGTGACCGCGCGCTTCTAATACGCC
+>megahit_ref_example_42_498_1:0:0_2:0:0_12b/1
+GGTTTTTTCAATCATCGCCACCAGGTGGTTGGTGATTTTGGGGGGGGCAGAGATGACGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATATCG
+>megahit_ref_example_42_498_1:0:0_2:0:0_12b/2
+GGATTAAAAAAAGAGTGTCTGAAAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAAT
\ No newline at end of file
diff -r 98242353faa4 -r de387b2b2803 test-data/interleaved_result.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/interleaved_result.fa	Mon Feb 18 12:14:46 2019 -0500
@@ -0,0 +1,2 @@
+>k59_1 flag=1 multi=8.7336 len=1215
+TGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCTTCGCCCAGTTCCAGATCCCTTGCCTGATTAAA
diff -r 98242353faa4 -r de387b2b2803 test-data/paired_result.fa
--- a/test-data/paired_result.fa	Mon May 14 06:11:34 2018 -0400
+++ b/test-data/paired_result.fa	Mon Feb 18 12:14:46 2019 -0500
@@ -1,2 +1,2 @@
->k141_1 flag=1 multi=107.0000 len=390
+>k141_1 flag=1 multi=106.0000 len=390
 CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG