| Next changeset 1:7157accd23d0 (2022-02-12) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a" |
|
added:
drep_compare.xml macros.xml test-data/Enterococcus_casseliflavus_EC20.fasta test-data/Enterococcus_faecalis_T2.fna test-data/Enterococcus_faecalis_TX0104.fa |
| b |
| diff -r 000000000000 -r ef1c257adcbd drep_compare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/drep_compare.xml Tue May 05 06:20:45 2020 -0400 |
| [ |
| @@ -0,0 +1,62 @@ +<tool id="drep_compare" name="dRep compare" version="@VERSION@.0" python_template_version="3.5"> + <description>compare a list of genomes</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + @PREPARE_GENOMES@ + dRep compare outdir + @GENOME_COMPARISON_OPTIONS@ + @CLUSTERING_OPTIONS@ + @TAXONOMY_OPTIONS@ + @WARNING_OPTIONS@ + @GENOMES@ + ]]></command> + <inputs> + <expand macro="genomes"/> + <expand macro="genome_comparison_options"/> + <expand macro="clustering_options"/> + <expand macro="taxonomy_options"/> + <expand macro="warning_options"/> + <expand macro="select_outputs"/> + </inputs> + <outputs> + <expand macro="common_outputs" /> + </outputs> + <tests> + <expand macro="test_defaults_log"> + <has_text text="dRep compare finished" /> + </expand> + </tests> + <help><![CDATA[ +**dRep compare** + +`dRep <https://drep.readthedocs.io/en/latest/overview.html>`_ performs rapid pair-wise comparison of genome sets. + +`dRep compare <https://drep.readthedocs.io/en/latest/overview.html#genome-comparison>`_ can rapidly and accurately compare a list of genomes in a pair-wise manner. This allows identification of groups of organisms that share similar DNA content in terms of Average Nucleotide Identity (ANI). + +dRep performs this in two steps: + + - first with a rapid primary algorithm (Mash) + - second with a more sensitive algorithm (ANIm). + +We can’t just use Mash because, while incredibly fast, it is not robust to genome incompletenss (see `Choosing parameters <https://drep.readthedocs.io/en/latest/choosing_parameters.html>`_ and `Module Descriptions <https://drep.readthedocs.io/en/latest/module_descriptions.html>`_) and only provides an “estimate” of ANI. ANIm is robust to genome incompleteness and is more accurate, but too slow to perform pair-wise comparisons of longer genome lists. + +dRep first compares all genomes using Mash, and then only runs the secondary algorithm (ANIm or gANI) on sets of genomes that have at least 90% Mash ANI. This results in a great decrease in the number of (slow) secondary comparisons that need to be run while maintaining the sensitivity of ANIm. + + +**INPUTS** + + - Genome sets in fasta format. + + +**OUTPUTS** + + - `Figures <https://drep.readthedocs.io/en/latest/example_output.html#figures>`_ that show the relationship of the Genome inputs. + - `Warnings <https://drep.readthedocs.io/en/latest/example_output.html#warnings>`_ report two things: de-replicated genome similarity and secondary clusters that were almost different. + + + ]]></help> + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r ef1c257adcbd macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 05 06:20:45 2020 -0400 |
| [ |
| b'@@ -0,0 +1,474 @@\n+<macros>\n+ <token name="@VERSION@">2.5.4</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">drep</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/ismej.2017.126</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+\n+ <xml name="genomes">\n+ <param argument="--genomes" type="data" format="fasta" label="genomes fasta files" multiple="true"/>\n+ </xml>\n+ <token name="@PREPARE_GENOMES@"><![CDATA[\n+ #import re \n+ #set $genomefiles = [] \n+ #for $genome in $genomes\n+ #set $input_name = $re.sub(\'[^\\w\\-_.]\', \'_\',str($genome.element_identifier.split(\'/\')[-1]))\n+ ln -s \'${genome}\' \'${input_name}\' &&\n+ $genomefiles.append($input_name)\n+ #end for\n+]]></token>\n+ <token name="@GENOMES@"><![CDATA[\n+ -g \n+ #for $genomefile in $genomefiles\n+ \'${genomefile}\' \n+ #end for\n+]]></token>\n+\n+\n+ <xml name="checkm_method">\n+ <param argument="--checkM_method" type="select" label="checkm method" optional="true">\n+ <option value="taxonomy_wf">taxonomy_wf (faster)</option>\n+ <option value="lineage_wf">lineage_wf (more accurate)</option>\n+ </param>\n+ </xml>\n+ <token name="@CHECKM_METHOD@"><![CDATA[\n+ #if $checkM_method:\n+ --checkM_method $checkM_method \n+ #end if\n+]]></token>\n+\n+ <xml name="filtering_options">\n+ <conditional name="filter">\n+ <param name="set_options" type="select" label="set filtering options">\n+ <option value="yes">Yes</option>\n+ <option value="no" selected="true">No (use --checkM_method taxonomy_wf)</option>\n+ </param>\n+ <when value="yes">\n+ <param argument="--length" type="integer" value="50000" label="Minimum genome length"/>\n+ <param argument="--completeness" type="integer" value="75" min="0" max="100" label="Minimum genome completeness percent"/>\n+ <param argument="--contamination" type="integer" value="25" min="0" max="100" label="Maximum genome contamination percent"/>\n+ \n+ <conditional name="quality">\n+ <param argument="source" type="select" label="genome quality">\n+ <help>\n+ --ignoreGenomeQuality is useful with\n+ bacteriophages or eukaryotes or things where checkM\n+ scoring does not work. Will only choose genomes based\n+ on length and N50. \n+ </help>\n+ <option value="checkm" selected="true">Run checkM</option>\n+ <option value="genomeInfo">User supplied genomeInfo csv file</option>\n+ <option value="ignoreGenomeQuality">--ignoreGenomeQuality (NOT RECOMMENDED!)</option>\n+ </param>\n+ <when value="checkm">\n+ <param argument="--checkM_method" type="select" label="checkm method" optional="true">\n+ <help>\n+ Using the checkm method of lineage_wf can require more than 40Gb of RAM.\n+ </help>\n+ <option value="taxonomy_wf">taxonomy_wf (faster)</option>\n+ <option value="lineage_wf">lineage_wf (more accurate)</option>\n+ </param>\n+ </when>\n+ <when value="genomeInfo">\n+ <param argument="--genomeInfo" type="data" format="csv" label="genomes fasta files">\n+ <help><![CDATA[\n+ A CSV dataset that must contain: [\n+ "genome"(history dataset name of .fasta dataset of that genome'..b'lt: ANImf)\n+\n+ -n_PRESET {normal,tight}\n+ Presets to pass to nucmer\n+ tight = only align highly conserved regions\n+ normal = default ANIn parameters (default: normal)\n+\n+]]></token>\n+\n+ <token name="@CLUSTERING_HELP@"><![CDATA[\n+CLUSTERING PARAMETERS:\n+ -pa P_ANI, --P_ani P_ANI\n+ ANI threshold to form primary (MASH) clusters\n+ (default: 0.9)\n+ -sa S_ANI, --S_ani S_ANI\n+ ANI threshold to form secondary clusters\n+ (default: 0.99)\n+\n+ --SkipMash Skip MASH clustering, just do secondary clustering on\n+ all genomes (default: False)\n+ --SkipSecondary Skip secondary clustering, just perform MASH clustering\n+ (default: False)\n+\n+ -nc COV_THRESH, --cov_thresh COV_THRESH\n+ Minmum level of overlap between genomes when doing\n+ secondary comparisons (default: 0.1)\n+ -cm {total,larger}, --coverage_method {total,larger}\n+ Method to calculate coverage of an alignment\n+ (for ANIn/ANImf only; gANI can only do larger method)\n+ total = 2*(aligned length) / (sum of total genome lengths)\n+ larger = max((aligned length / genome 1), (aligned_length / genome2))\n+ (default: larger)\n+\n+ --clusterAlg CLUSTERALG\n+ Algorithm used to cluster genomes (passed to\n+ scipy.cluster.hierarchy.linkage (default: average)\n+\n+]]></token>\n+\n+ <token name="@SCORING_HELP@"><![CDATA[\n+SCORING CRITERIA\n+Based off of the formula: \n+A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)\n+\n+A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight:\n+ -comW COMPLETENESS_WEIGHT, --completeness_weight COMPLETENESS_WEIGHT\n+ completeness weight (default: 1)\n+ -conW CONTAMINATION_WEIGHT, --contamination_weight CONTAMINATION_WEIGHT\n+ contamination weight (default: 5)\n+ -strW STRAIN_HETEROGENEITY_WEIGHT, --strain_heterogeneity_weight STRAIN_HETEROGENEITY_WEIGHT\n+ strain heterogeneity weight (default: 1)\n+ -N50W N50_WEIGHT, --N50_weight N50_WEIGHT\n+ weight of log(genome N50) (default: 0.5)\n+ -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT\n+ weight of log(genome size) (default: 0)\n+\n+\n+]]></token>\n+\n+ <token name="@TAXONOMY_HELP@"><![CDATA[\n+TAXONOMY:\n+ --run_tax generate taxonomy information (Tdb)\n+ (default: False)\n+\n+ --tax_method {percent,max}\n+ Method of determining taxonomy\n+ percent = The most descriptive taxonimic level with at least (per) hits\n+ max = The centrifuge taxonomic level with the most overall hits\n+ (default: percent)\n+\n+\n+ -per PERCENT, --percent PERCENT\n+ minimum percent for percent method\n+ (default: 50)\n+\n+\n+ --cent_index CENT_INDEX\n+ path to centrifuge index (for example,\n+ /home/mattolm/download/centrifuge/indices/b+h+v\n+ (default: None)\n+\n+]]></token>\n+\n+ <token name="@WARNINGS_HELP@"><![CDATA[\n+WARNINGS:\n+ --warn_dist WARN_DIST\n+ How far from the threshold to throw cluster warnings\n+ (default: 0.25)\n+ --warn_sim WARN_SIM Similarity threshold for warnings between dereplicated\n+ genomes (default: 0.98)\n+ --warn_aln WARN_ALN Minimum aligned fraction for warnings between\n+ dereplicated genomes (ANIn) (default: 0.25)\n+\n+]]></token>\n+\n+\n+</macros>\n' |
| b |
| diff -r 000000000000 -r ef1c257adcbd test-data/Enterococcus_casseliflavus_EC20.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Enterococcus_casseliflavus_EC20.fasta Tue May 05 06:20:45 2020 -0400 |
| b |
| b'@@ -0,0 +1,48964 @@\n+>gi|478483683|ref|NC_020995.1| Enterococcus casseliflavus EC20, complete genome\n+AAAGTATTTTTTTCTAACCTTTTTTATCGTAATCTGTGGAAAACTTTTTCAATCCGTGCTATTTTAGTTA\n+TATCTATTCTTAGTTATAGGAGGACAATTTATGCCATCTGCTGATTCTATTTGGCAAGATCTTCAACGTT\n+CCTTTAAAGAAGAGCTGAATCCGGCCAGTTATAGTGCTTGGATCGAGACTGCCAATGTCTTGTCGTTTGA\n+AAAAAATCAGCTGCTGATCGAAGTACCCAGCGATCTTCATAAATCTTATTGGGAAAAAAATCTAGCTGCC\n+AAAATTGTTGAAATGGGATTTATGAAAACTGGTGAAGAATTGATTCCTAGTTTTGTGACTGTCGAAGAAG\n+CAGAAGCTTTAAAAACAGCCCCTTCTACTATTCAAACAGCTGCAGAAGAAAACGAGCGGCCGCCGAAATC\n+GATCTTAAATGAAAAATACACATTTGATACCTTTGTCATCGGGAAAGGCAATCAGATGGCCCACGCTGCT\n+GCTTTAGTTGTTGCAGAAGATCCTGGGTCTATTTATAATCCGCTGTTCTTCTATGGTGGCGTTGGTTTAG\n+GGAAAACCCACTTGATGCACGCGATCGGTCATCAAATGTTGCTGAAACGTCCCAATGCCAAAATCAAGTA\n+TGTTAGTAGTGAAAATTTCACCAATGATTTCATTACTTCTATTCAAAAGAACAAAATGGAAGATTTTCGA\n+AACGAATACCGCAATGTTGATCTTTTGCTGGTGGATGATATTCAATTCTTAGTCAATAAAGAAGGAACCC\n+AAGAAGAATTCTTTAATACCTTCGAAGAACTGTATCGCAATAATAAACAGATCGTTCTGACAAGTGATCG\n+TTTGCCAAATGAGATCCCGACTTTGCCGGAACGTTTGGTTTCCCGTTTTGCTTGGGGCTTGTCCGTTGAT\n+ATCACCCCGCCGGATCTAGAGACGCGGACTGCGATTTTGCGGAAAAAAGCCGAAGCCGAACGCTTGGAGA\n+TCCCCGACGATACCTTAAGTTATATCGCTGGGCAGATCGATTCGAATATCCGAGAACTTGAAGGAGCACT\n+CGTGCGGGTGCAAGCTTTTGCTACGATGCAAAACTCAGACATTACAACGAGCTTGGCAGCTGAAGCCATC\n+AAAGCCTTAAAATCAAGCCATGGCTCGACCCAAGTTTCGATTTTGCAAATCCAAGAAGAAGTCGCAAAAT\n+ACTATCACATTCATGTCAATGATCTAAAAGGGAAAAAACGGGTCAAAGGCATCGTGGTTCCACGGCAGAT\n+CGCGATGTATCTCTCTCGAGAATTGACCGATAGTTCTTTACCAAAAATCGGCGGCGAATTTGGCGGCAAA\n+GACCATACAACGGTCATTCATGCCCATGAAAAAATTCAGCATTTAGTCGAAACAGATCCCACGATCAAAA\n+ATGAGATCGCTGAAATCAAACAAATCCTCTTCAGCTGATCTGTGGATAAGAAAAGAAGAACCAAAAAAGT\n+TGTCCACAAGTTATTCACAGGCATTTTCGTTAGTCTAATCACTCTTTTCTCGAGTTATCCACATTACTAA\n+CAAGCCTATTACTACTATTACTTTTATTTAATAACTATAAATTAAAGGAGTATCGCTATGAAGCTAACTT\n+TAAACCGAACAGAGTTCATGCAAGAATTACAAACTGTCCAACGGGCGATTTCAACCAAAACCACCATCCC\n+GATCTTAACTGGAGTAAAATTATCCCTTTCAGAAAAAGGATTGACCATGACTGGGAGCAACGCCGATATT\n+TCCATTGAAACTTTTTTAAGTGTGGAAAACGAAAAAGCGCAAATGCAAATCGAAAAAACAGGAGCGATCG\n+TTTTACAAGCACGTTTCTTCAGTGAAATCGTTCGTCGTTTGCCTGAAAGTACCTTAACCTTAGAAGTATT\n+AGACAATAATCAAGTAGCGATCACTTCTGGAAAAGCCAACTTTACCGTCAACGGCTTGGATGCCGATAGT\n+TATCCACATTTACCAGTTGTCGAAAGTCAAGATTCGATCGAGATTCCAGCGCACGTGTTGAATAAGGTCG\n+TTAGTGAAACAGTCTTTGCGGTTTCGCAACACGAAAGCCGTCCGATCTTGACTGGGGTCCACTTTGTCTT\n+AGAAAATCAAAAATTATTAGCTGTTGCGACGGACTCACACCGTCTGAGCCAACGGGTGATTCCATTGGAA\n+AGTGGAGAAACAGCCTTCAACATCGTAATTCCTGGCAAAAGCTTAACGGAACTTTCTCGTTCCTTAACAG\n+ATGAAGAAGAAGCGATCCAAATCAGCATTATGGATAACCAAGTGTTGTTCCAAACGAAAACCATGAAATT\n+CTATTCTCGTTTATTGGAAGGAACTTACCCAGATACCAACCGTCTGATTCCTTCAAGCTTCAATACTGAG\n+ATTGAATTTTCTGTCCCAGAATTGTTACAAGCCATCGAACGGGCGTCATTGCTTTCTCATGAAGGCCGTA\n+ATAACATCGTTCGTTTGGCGATCTCCGAAGAAGCCGTTGTCTTATATGGAAACTCACCAGAAATCGGGAA\n+AGTCGAAGAAGATCTTTCTTTTGAAAAAGTGACCGGCGACCCATTAGAGATCTCTTTCAATCCTGACTAT\n+ATGAAAGCAGCACTACGAGCATTTGGTGACACCAGCATTGTGATCCGCTTTATCTCAGCGATCCGTCCCT\n+TTACATTGGAGCCGACAGAGAGCAAAGGCAGCTTTATCCAGCTGATCACACCGGTGCGAACCAACTAGTT\n+TTTCATGTCTTTTGAAAAAAGTTGAAACAATCATCTGAAAATGAATAAATGAGTTAAAAGGGCTTAAAAT\n+CGTTTTTAAGCCCTTTTTTCTATTTTGGCTTCTTTTTTGTCTAAAAGCAGTAAGTCTTCTGAGAATGAAA\n+AATATGCCGATGAATTTGTTTTCTTGGCAAAAAAAGAGTATAATAGAGCTAAACGCTCTTTGATAGAATT\n+GAGGGGAATTATGAAAATGCAAATACCGTTAGAAACGGAATACATGACACTTGGACAAATGCTCAAAGAA\n+GTCAGTGTGATCAGCAGCGGCGGCCAAGCGAAATGGTACCTTGCAGAGCACACCGTTTTTGTCGACGGCG\n+AGCCAGAAAATCGACGAGGGCGCAAATTGTATGCGGGAATGCGTGTTGAGCTACCTGATGAAGGTACTTT\n+TTTTATGGTGAAGAAGGAAGACGCCGATGCGCCTGAATGAGTTGCATTTAAGCAATTATCGGAACTATGA\n+TTCGCTGACACTGACTTTTGAGAAAGGTCTGGTCATTTTTTTAGGCGAAAACGCGCAAGGAAAAACCAAT\n+ATTTTAGAAAGTATCTATGTATTGGCGATGACCAAAAGCCACCGCACCTCCAGCGAGCAAGAGCTTATCC\n+GCTGGGACACAGAAGGTGCGCGGATCTCTGGCAGTGTCAGTCGGGGACGCTCAACGATCCCGTTAGAACT\n+GTTTTTGTCAAAAAAAGGACGAAAAACGAAAGTAAACCACATTGAGCAAAAAAAGCTCAGTAGTTACATA\n+GGGCAGTTGAATGTCATTTTATTTGCTCCAGAAGACCTCTCCCTTGTAAAAGGAAGTCCCCAAGTCCGCC\n+GTAAATTTCTCGATATGGAAATTGGGCAGATCGATCCAATCTATCTCTATGATCTCGTTCAATACCAATC\n+CGTTTTGAAACAGCGCAATCAATACTTAAAACAGCTGAATGAAAAAAAACAGACCGATGAGATCTATTTA\n+GATGTTTTGACGGAACAGCTGGTGGCTTTCGGCAGTAAAATCATTTTAGCCAGACAACGATTTGTTCAGC\n+GCTTGGCGT'..b'ACTGCGAGATTCATCGCCTTATCGGTCT\n+TGGCACGAATCAGGTCCATCACCGCCTCGGCTTGAGAAAGGTCAACCCGTCCGTTTAAAAAGGCCCGCTT\n+CGTGAATTCTCCCGGCTCAGCCAACCGTGCGCCTTGTCGCAAAACCAGCTGCAAGAGTTGATTGACGACA\n+ACGATCCCGCCGTGGCAGTTGATCTCAACGACATCTTCTCGGGTAAAGGTCCGCGGCTTTTTCATCACTG\n+ATAGCATCACTTCATCCATCAAACGGTTTTCTTCTGGGTCTACGATATGACCATAATGGATCGTATGACT\n+AGGGACTTGGGCGAGGGTTTTAGTGCCTGCTTGAAAAATCCGATCCGCAATTGCGATCGCTTTTTCCCCG\n+CTTAATCGCACAATACTGATGGCCCCTTCGCCTGGCGGGGTGGAAATCGCGGCAATCGTATCAAATTCTT\n+GCGTTATATTCGCCATGTTGCTTGCTCCTCCTATTTTTTCACATAAAAAAAGTGCCCACTCCACCCGTCA\n+AATTGATTGAAAATCAATAAAAACGAGTAGACTTAGCACTTTGACTGCTTGTCAATTAAATTCTGGAAAT\n+AGATTAGCACATTTTTGCGTGAGTCGCAAGCTTCCTTCAAAAACTTTTAAATTTTGCATCTGTCCGCAAA\n+AACCTTTAAAATAAAAGCAAAGAATAAGAAAAGAGGGATCTATTATGGAAACCATCAAATCATCAAACAG\n+CGCTGCTCGCATTAAAGAAATCATTTTATCGACAGGAAACGTGAATCGGCCTTACGTCGTGCGGGATATC\n+GTCTTTGCGGCAGACAAAATCGAAGTAGATCTATTTGATACATCTGTGAATTTGAACGATCTGTTGGCAG\n+ATGTGACCTATCGCTTAAAAGAAACCGCCCACAGCTACGGAGCGAATGCAGTGATCAACTGTCATTTCGA\n+ACATGACCGCATCGTCGAAGGCGACAAAACCTACCTTGAGATCTTTGCCTATGGTACAGTGGTTCAATTT\n+ACTCAATCAACCATCGGCGGCTAATTGCCTCTATCATCAAAGAAAAATACAAAAAAGAGTCCGCGGCATA\n+CGGACTCTTTTTTGATACCAAAGGCTGACCTACGTAACGTATGTTGACTTTGATAAGAATGATTTCTAGT\n+CAAGGATACTTGGTTTTAAATTTGTTGTCAATCGCTTTTTCCCATCAAAAAAGGGAAAGGCTTGTCAGAC\n+CGCCTTTCCCTTTTTTCATTAAATTCGTTTGTCCGCAGGTTCCACTACTAAGTAGCGATACGGTTCATCC\n+CCTTCAGAATGAGTTTGAACATACGCATCTTTACTCAAAACTGAATGGATCTGCTTTCTTTCAAACGCCG\n+GCATCGGTTCTAAAAAGACTGGGCGGCCTGTTCGTTTGACTTTTTCAGCAGTACGGCTAGCCAAACGTTC\n+TAAGATCGCTTGACGTTTTTCACGGTAATCTCCGACATTCACTACAATCGACAATTTGTTTTTCGCGATG\n+CGGTGAATATACACTTGCGCCAAATATTGCAGTGCATTCAAGGTTTTGCCGTGCTTCCCAATCAAAATGC\n+CTTGTTTTTGCGTTTCTAAATGAAAGACGACCACGCCGTCTTGACGAGCGGTTTTTACTAAGGCGGGTGC\n+ATTCAATGCTTTTGAAATATTTGTCAGATAGAGTCCCAGCTGAGCCAGCGCTTCCTCATCTGAAAGATCC\n+GTCAGCAAAACAGGTTCGCTCGCTGCTGCTTCCATCACACTGCTTGCATCCTCTGTCGTCACAGGATCTG\n+GTTCTACCAGCGGTTTTGCTGGTACTTCTTCAACGGGTGCCGGTTCTTCAACGATTCGTTTTTCAATGGA\n+GACCCTTGCTTGTTTTTTTCCTAGACCCAAGAAGCCTTTTTTTCCTTCATCCAGGACTTCGATTACTGCT\n+TGATCTTTGGTGATACCAAGGACTTGCAATCCCTCTTGAATTGCTTCATCTACTGTCAGATTTTCATAAA\n+TCGGCATTGCAGTGCAACCTCCTCTTATTTTTTCCGTTTCTTTTTAGGACTCATTGCTTTTTTCAGCGCA\n+CGTTCACGCTCGCGTTCTTTGCGGGCAGCTTCTTCTCTTTCTTGGCGAATCTTGAATGGGTTATTTAAGA\n+TCATTGTTTGCACAACTTGGAATGCATTGGAAACGACCCAGTACAAGGAAAGACCGCTGGCAATGTTGAT\n+CCCCATCAGTAAGATCATCATCGGCATAGCGAAATTCATGATTTTCAGACTCGCATTTGATTCCACTTGG\n+CTCATACTTGATAAGTAAGTACTTGCAAAAGTAAAGAGCGCCGCTAAAATCGGCAAGATGAAGTATGGGT\n+CACGATCACCCAGCTGCAGCCATAAGAATTTTCCTTCTTGCAGAGCAGGAACCCGTGAGATCGATTGCCA\n+CAAGGCCATCAAAATCGGCATTTGTACCAATAATGGCAGACAGCCGGCATAAGGATTGACATTGTTTTCC\n+GCATACAAACGTTGTGTTTCTTCTTTTAACTTGCTTTGTGTTTCTGTATCTTTTGACGCATATTGCTGTT\n+GCAGCGCTTTTAGCTTCGGTTGTAATTCTTGCGTTTTGCGCATGCTTTTGGTTTGGAAGTGCATCAACGG\n+CATCAAAATGACCCGAATGATCAATGTAAAGAGGATGATCCCGATCCCGGCATTGCCAAAGGAGAGGGCT\n+TTGATCGCCTCTGCAAAATAATAAACGATGTAACGGTCCCATAGACCAGTACTTTGTGCATTTACTTCAC\n+CTGTTGCACCGCAGGCAGATAAGACAACTACTAATGAGAGGACTCCCAAAAATAGTAAGACGCGTTTCCC\n+TTTTTTCACGTAACTAATTCCTTTCCATTAATGAATAATTTTGGCAAGTTTTAAGACATGCTCTAAATTC\n+GAGTAGATTTCCTTTGAGGAACAAGTGGCGATACTTGGACGGGCGATCACGATGAAATCGACCGCTGGTT\n+CGATTCGCGGCTTCATTTCCGTTAAACTTGCACGGATCTTGCGCTTGATCTCATTTCGCTTCACTGCATT\n+ACCGACTTTTTTCCCTACAGATAAACCAACTCGAAAATGTGATTGCTCTTTAGGTAAGACATACACCACG\n+AACTTCCGATTTGCAAAAGAATTTCCTGCCTGAAAAACTTTTTGAAAATCTTGCTCTGTTTTTACTCGAT\n+AGGATTTTCTCATCTTCGGTTCCTTCACTTCTTTCAATTAAGCTTCGCGAAACGGATTGAATCCGTAACC\n+ACTCACCTGTCAATAATACCATATTTGCCAAAAGTCAGACACTATATTCCGCAAAAACGGCATAAAAAAA\n+AACCACTGGCATTCAGTGGCTTACGCAGAAATAACCTTTCTGCCTTTACGACGACGGCTAGCTAAAACAC\n+GACGTCCATTTTTTGTACTCATACGTTTACGGAATCCGTGAACTTTTTGACGTTTACGTTTATTTGGTTG\n+ATACGTTCTTTTCATTTATTTCCACCTCCATCAGGATAATGCTTATGCGCACAGACATACTTTGATAGTA\n+TAACGAGTCAAGTACTAGTTTGTCAATAAGAAGTTTGCTCAAAATCAGGCATTCTTTATCCACAATCCCT\n+TTGATTTGTGTGGGTTTACTGTTTATAGCCAATTTTTGTGGATAACTTTTTCCCCAGAGTTATTTTGGCT\n+TTTTCCACAAACAAGCAGCCTGTAGAAAAGTTTTCCACAATCACTTTTTTAACTGTTGATAACTACCCCG\n+AAACCTAGTGTTATCAAGGTGTGATCTTCACATCGATCTGTGGATAAAGGAGATTGTTTTACAGTTATGC\n+ACATTCTTTTTCTACCTGTGGATAGTCGGATTTCGAACATGTGCATTTCCATTTTTCTTTTATCCCGTTT\n+TGTGGA\n+\n' |
| b |
| diff -r 000000000000 -r ef1c257adcbd test-data/Enterococcus_faecalis_T2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Enterococcus_faecalis_T2.fna Tue May 05 06:20:45 2020 -0400 |
| b |
| b'@@ -0,0 +1,40833 @@\n+>NZ_GG692854.1 Enterococcus faecalis T2 plasmid scaffold supercont1.22, whole genome shotgun sequence\n+TAAAATTAATGTGCCAGTCTTTTTTATCAAAACACCTATTAATAGAGGGGTATTTGAAGAGATCTTCGGCGAAACATTAA\n+AAGGATAGGGTGAAAAAAATGAGTAATAAAAATGAACACGGGTTTTGGGAATGGCTACAAATAGACTACTTTTCAAGGTT\n+TCCAGATGCAACGAATGATGATGTGACTAAATTCTTGTTACGCTTTACAGAAGCTAGTAAAAATTCAACCAAAGAAGGAT\n+CAAAAATCATTGAAGAATTGTTTGAGGAAGAACGAAAACGCAGAAAAGGACGGTGATTTTTCGATGAACGAACGTGAAAA\n+AGATATAAAAAAGTGGCTTTGCCAGTTATTAGATCAGACCTACCTAAATGCGGAAGCGTATAAAAATTTTTTTGTAAGAG\n+TTCTTCCAAAACAGCGTAAACGGACACTTGGTAACTATTTAGAAGTAGAACGTGTATTAGAAGTGAGCAATTTGTTACGA\n+GAGCCTGTGGAAGTCATGCTGACACTGATACGCTTATTAGCTGCTCATATTGTTGTTGTTAATCGTGAGCAATTTCAAGA\n+GGAAGAAGCAAAAGAGAAAATAGTGAAGGAATTATTAGGGGAATTGCTTAAGCAAGGGAAAATTAGTCAAAAAGAACAAA\n+CAATTATGTTAGGCACTGGTTTTTTAGAAGAAGAAACTGCTCTTTATGGCGAGTTAGAAAGTTGGGCGACTGATGCGAAA\n+GAAACCATTTATTGTACGGTAGTTGAGAATGGCTTCCCTATTAAAATGGAGTTACACAAACTTGGGTATCAATGGCTAAA\n+AAGTCGCCAAGCTTGGGTGAAAAGTTACGAGACACAAGAAGCTGCTGAAGTCGCCAAAGGTCAGCTTTGGGCATTAAGTA\n+GTGAAATAGAAGTTAGTGTAGAGACACCGATTACTTGTTTGTTTCATTTTGATTATTATTTATCCGTTAAGCCAGCGGAA\n+CGTTACAATGAAACGATTGTTGCTTTTGGGTATATCTATGAAAATTACGGCTTTAAAAAGAAATTTGTCAAACAAGTACC\n+AGTAAAAGATTTTTCAGGAGAACGTGAGCGTTTAGCACGATTAGAAATTCCTTTTGAACTAGTAGTACCAAAAGAAAGAC\n+AAGTGATTTATTGACTATTTAAGAATAAATTAGGAGGAATAACAATGGCAGTGAAAATTGATGGAACGATAAAAAAACGT\n+GTTCAATCTTTAATGGCTTTAAATGGACAGTCTTATGAAGAATGGCTTAATAATCAGCACCAAAAGTATTTAAATGAACA\n+ATCAGAAGTCATTGACCGACTATTGAAAAAAGAATTGGAACGGAAAAAAGGAACAAATGAATAGTTAAAGTAAGTAGAAT\n+AATTTAGGAGGAAATCAACGTGAAAAACAAAATTAAGAAAAAAGTGAAGTATTTTACAGCTGTAATTCAAACGATTATTG\n+GTCTTGGATGGATTGAAGTGAGTACGATGATGCCGGCATTTGCCGATGTTGAACGAACAATTCAAGGCGTTGAAACTGGT\n+TTAGGATCGGAATTTAAAAAGTTTGCTAATCCGGCATTAGGTATAGCAGTCCTCATTTATGGAGGAGCTAGATTTATGGG\n+ACATGATATTGCACAATGGGCAAAAAAATGGGTTTTCGGAGCATTTGTTGGTGCAGCAATTATTGTGAACTTTACTTGGA\n+TTAAAGATACTGTTTGGGGTTGGTTAGGAGGTTGATTCTTAAATGACTGTAGAAGTGGAGATTTTATCGTCTAACGTTGA\n+AGTCTTAGAAAAACAACCACCGTTGGAGTTACTTCCCTTCGCAGATTTTATTGAAATCACAAGATGCATGTATGTTAAGG\n+AGGCAGTAACTTTCCAACTATTGGAAGTTGGTGGAGATCCTTTTTATCGGGGAAGTTTTGAAAAATTAAATGATGAATGG\n+ACACTAGAAAAAGATATACAAAAGAAGTTAAATCAACTAGTCAAAAAAAAGAAAATGACGGCAGAGCAGGCGGAGGGCTT\n+ACTCTACAAAATTCCTTTTAAGAATCTACAGGAGGCTAGTTTTTCGAACGAAAAGAAAACGAGATTCTTCAAAAAAGAGA\n+AGAAGCCCAAAAATACCCAAAAAGTCGGGAGGCTTAAAAGGAAAATACACGTTATTTCTCCAATAAAACTTTCCCAGAAA\n+CAATTGAGAATTTTAGGAGTGTTTGTGATAGGAATACTCTTAATTGTGATTGGTTGGAAATTTATGGCGGGAAGTCAATC\n+GACGGCCAAAACTAGTTTAGAACCTACGTATCAGCAGTTAGTCAATAAAGAAAAGTACGCTGAAATAGTAAAAAAATATC\n+CTGAGAAAGAACCAGAGCTAATTGAGGAGTTATTTCAAAAAGAAGATAAAGCTGGTTTGAAAAAAATAGCTGAACACTCT\n+AATACACAGTTAGCTCAGCTATATCTTGCTTTTTTAGACAAAGATTGGCAGAAAGTAACAGAACTTTCCAAGTTACCACA\n+GGATAGTGATGTTCAAGCAATGGTAGGCTATGCTTTTTTAGAACAAGGTAAGATAGAAGAAGCAAAGCTTATTAATAAAG\n+AAATTCAAAACGATACGCTAACAAAACAAATCAAAAGTAAGGAAATCGAACAGGCGTATAAACTTCTTAGAGAGCGAAAA\n+ATATCTGAAGCGGAGAGAATAAACGAAAGATTGAAGGATAATGGATTATCCGAAGCAATTAAAGTAGCCAAAAGTATTCA\n+TAACTTGTTAGAAAAATACGCCAAAGATAAGGAAAATAAAGAATTATCAGAAAACGAGCGAAAAGAAGCTGCTGATAATT\n+ATCAGCTATGGCTGAAAAATTTGGAACAAATTGGTAAGTCTGTTCATTAATTCGGAGGATAAAATTATGAATGAATTTAC\n+GAATTTCAACTCTTTGTTCCACTGATTACTTTTACGGATTAGATAAAAAAAGAGCGAAAAATGTGATATAATCACCAAGA\n+GTAAATGGAAGTTGAAGACGGTAGCATAAATCCACCGCAAAGGAGCTGGTGCCTATGAGAGTACTCATAGTAAATCAGAA\n+AAACTGGCAAAGGAGTTGTGCAGTTGTGTCTGTATTAGAAGTGTTGGCCTTGCTTACACTATTAATACAAGTCTATAAAT\n+TAGGCAAAAAAGACGACAACAAAAAAGACCGTCGGTAAACTTTAGCAGGTTTCGACGGTCTTTTTTTGATTGTTGAAATA\n+TATGCTGCCGATCTTCTATCGGTCATTTACTCTAAGGGGACATGTTTCGAGCATGTCCTCTTTTCATAATCTATTATACG\n+TATAACGAACGAGAAAGTAAATAAAAAAGCAAAAAAAGGGCTGTTCTAAAAAGAATAGCTCTTTTTTTGTACACAACAAT\n+TGAGAGGGATGAAAGAAATGAACGGAAATCAAAAAGAAACCGCTAAAAAGCAGCATAAATATCTAATTATTGGATTATGT\n+TCAGTTGCGTTACTAGGAAGTGGCTTGACGTATGCCGCACTCAACCAGGGGGAAAAGAAGGAAGCACAGACAGAGCAACA\n+AGGTACAAAACCTAAAGAAGAGCGTCAAACACCAAAAAGTAAACAGTCCCCTTGGGAACGGAAAGTGACGGAGAATGAAG\n+AAAAAAACAAGGATAAAGACAAAAAAATTAAAAGTAAGCAGCCACATAAAACAAAAGATTCGTTAGCAGAAATAGTTAGC\n+GGTTTTGAACGTACAAAAGAAGAAAAACCAAAACTTTTTGGTGTGGAGATACCTGAAATAAAAAGCGATTTATTAGGACA\n+ACTAGCGAATGCTCTTGTTCA'..b'TGAGA\n+ACTACATTTATTATTACAATCATCACCGAATCAAGGAAAAACTTAACTGGAAAAGCCCAGTAGAATTTCGACAATTCAAT\n+CAAAAAACTGCATAAAAATAGAGTGGAAAAATCCACTCTA\n+>NZ_GG692836.1 Enterococcus faecalis T2 genomic scaffold supercont1.4, whole genome shotgun sequence\n+GAAAAGAGTTCTAAATGATAAATACAAACATGCACTAGAGCTAATGGAAACAAACAGCATGCGAGAAGTGGAACGAAAAA\n+CAGGTATTTCTTTGTCTACTCTCAAAAGAATCAAGAAACAAGCAAAGGAAGAACAGTTACTTAATGAGAAATAATTCAGG\n+AGTAGTTATTATGGAAAATAGAGAGAAAATTATTCAGTTGTTGAAGAATCCTTTAGTAACAGGTTATGGGATTGAGATGA\n+TGTCAAATGGGCGACTCTATTCAGCGAACTTTCAAAGATATAGGAATCGGATGAAGAAAGAAGAAAATCCAATGATTATC\n+TTTGATACTATGACTGAAAAAGTTGAAAAGGTATTTTTAGAATTAGCTGAAGAAGTCATACGAACGAACCCTAAAACAAA\n+ACAAGAATTCAAAGATATGATTAAAGAATATAGTTATAAGGAGGATAACAAATGGTAGTTCGAAAAACATATGATCATTG\n+GGGGATCGAAATCAGCACATGGAACAAAAGTAATATAGTTACTTTTATTGATTGTGACTGCGGTCAATTAGCTAAAAGAG\n+AACTAGGAAAGTATAATCAGTATAAATGTGATAGCTGCAATAAAGAATACAAATTGTATCAAGGCAATTATATCGCAATT\n+GATGAAAAAATAAATGAAGTAGCTCAAAACGATTGAAAAAGTAAAAAAGATTTTTGATAGTGTGATAGTGTGCTTTCAAT\n+AATT\n+>NZ_GG692835.1 Enterococcus faecalis T2 genomic scaffold supercont1.3, whole genome shotgun sequence\n+TCAGAATGGTGCATCCCTCAAAACGAGGGAAAATCCCCTAAAACGAGGGATAAAACATCCCTCAAATTGGGGGATTGCTA\n+TCCCTCAAAACAGGGGGACACAAAAGACACTATTACAAAAGAAAAAAGAAAAGATTATTCGTCAGAGAATTCTCATGTTT\n+GACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGCAGTCAGGCACCGTGTATGAAA\n+TCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCATAGGCTTGGTTATGCCGGTACTGCC\n+GGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGCCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGC\n+AATTTCTATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGA\n+GCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCAC\n+CGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCA\n+TGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGG\n+>NZ_GG692834.1 Enterococcus faecalis T2 genomic scaffold supercont1.2, whole genome shotgun sequence\n+AGCCCTTCAATCGCCAGAGAAATCTACGAGATGTATGAAGCGGTTAGTATGCAGCCGTCACTTAGAAGTGAGTATGAGTA\n+CCCTGTTTTTTCTCATGTTCAGGCAGGGATGTTCTCACCTAAGCTTAGAACCTTTACCAAAGGTGATGCGGAGAGATGGG\n+TAAGCACAACCAAAAAAGCCAGTGATTCTGCATTCTGGCTTGAGGTTGAAGGTAATTCCATGACCGCACCAACAGGCTCC\n+AAGCCAAGCTTTCCTGACGGAATGTTAATTCTCGTTGACCCTGAGCAGGCTGTTGAGCCAGGTGATTTCTGCANTAGCCA\n+GACTTGGGGGTGATGAGTTTACCTTCAAGAAACTGATCAGGGATAGCGGTCAGGTGTTTTTACAACCACTAAACCCACAG\n+TACCCAATGATCCCATGCAATGAGAGTTGTTCCGTTGTGGGGAAAGTTATCGCTAGTCAGTGGCCTGAAGAGACGTTTGG\n+CTGATCGGCAAGGTGTTCTGGTCGGCGCATAGCTGATAACAATTGAGCAAGAATCTTCATCGAATTAGGGGAATTTTCAC\n+TCCCCTCAGAACATAACATAGTAAATGGATTGAATTATGAAGAATGGTTTTTATGCGACTTACCGCAGC\n+>NZ_GG692833.1 Enterococcus faecalis T2 genomic scaffold supercont1.1, whole genome shotgun sequence\n+GGGAGCGTCAATAATTTTGTGTAAATAAATTGTCCTCCTGCAAAATAATTAGTTACTCAGTAAACATTGAAACTAATGTA\n+TCGGTTACCTGTTGAAAACCTTTATGGCTTCTGTTTAGAAATTTTTGATTGTATGTATCAAAAATGCTGACTAGAAAGCG\n+TTCTAGTGATTCTTCATTTTGAAACTGCTCTTTTCTACGGCTGTATCTTTTAATTTGCTTATTGAAAGACTCGATTAGAT\n+TGGTTGAGTAAATGGTTCTACGAATGCTAGGTGGAAAATCATAAAAAGTTAATAAGTCTTGGTTTTCTATGAGTGACTGC\n+GTCACTTTAGGATAGTTTTTCTTCCATTTCTCAATCATGCCGGATAAGAAGGTATTCGCTTCTTCTTTTGAGTTAGCTTG\n+ATAAACAGCCTTAAAGTCATCACAGATTTCTTTTCGGTCTTTGACACGTACTTTATGAGCGATATTACGAGATACATGGA\n+TACAACAATGCTGATATTTTGCTTTAGGATAAATTTGATGGATAGTATCTTTCATGCCTTTTAAGCCGTCCGTAATAAAA\n+AGCAAGACTTCTTGAACTCCTCTGGAGTTAATATCCTGTAGCAGCTCATTCCAAACGTATGTTGATTCAGTTGGAGCAAT\n+CGCATAACTCAGTACTTCTTTAGTGCCGTCTTCTCGTATACCAATGGCAATATAAATCGCTTCTTTGGATACGGTTTGAC\n+GTTTTAGTGGAATGTAAGTAGCGTCCATAAAAATAGCGACATACTTATCATTTAAGGCTCTGGATTTAAAGGCATTTACT\n+TCTTCAGTCAGAACTTTAGTCATGTTGGACATGGTTTGTGGAGTATAGTGATGACCGTACATTTTTTCGATCAAATCAGC\n+AATTTCAGACATCGTAACACCTTTTTCGAATAAATGGATAATAGTGGTTTCCAATGTATCGTTTGTTCTTTTGTAGGCTG\n+GTAAAGTTTGTTGTTTAAACTCACCATTACGATCTCTAGGTATTTCCAATGTTAATTCACCATATTCGGTTTTGATTGAT\n+CGAAAGTAAGAACCGTTTCTCGAATTACCTGAATTAAAACCAGTGCGATCATATTTTTCGTAATCTAAAAAAGCCGTTAA\n+TTCAGTCCGTAGGAGTGTGTTTATCGCTTTTTCTAAGTGCGAACGGAATAATTCATTTAAATCGCCTTTAGTGACTAGAG\n+TTTGCACAATTTCTGTAGTAAAATCATTCATAGGGAAGTCCTCTTTTCTGTGAATTGGTTGTCGTTAACTTTATTCTACA\n+GAAGCGACTTCCTTTTTTGTATGGATTTTTTCATTTACACAAAATATTTTACACTCTC\n' |
| b |
| diff -r 000000000000 -r ef1c257adcbd test-data/Enterococcus_faecalis_TX0104.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Enterococcus_faecalis_TX0104.fa Tue May 05 06:20:45 2020 -0400 |
| b |
| b'@@ -0,0 +1,39594 @@\n+>NZ_GG669016.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD95, whole genome shotgun sequence\n+TTCAAGATAAGTTTTAAGTCTGTGTCCTTACACGAGATTTTTTACGCAAAAATAATTCTTTGTAGTTCATCAGCACAAGC\n+ACATTTTTATATAACTGATTAATTTTGTTGAATTATAGTTATATCTATATTGATTAATAGCTGATCTTGCTAAGCATGGA\n+TTTAATAAGAATATTTTTGTTAAAAAATCATATAACCTTACGT\n+>NZ_GG669015.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD94, whole genome shotgun sequence\n+ACAAAGAAAGAGAATAAATAAATGAGATAGGAAGTGTTTCAATTTTTTTGTTACGAGTAATCCAAGAAGAAACAGTTCCT\n+TGAGAGAAAGCATGTAATTCACAAAATTCTTCTACAGTAATCCCTAGATGCTTGATAATGTATGCGTTGATAGGGTGTGG\n+ATATACAAAGGTTTTTCTAGGCATGGTGGGTAAGTTTCCTTTCTT\n+>NZ_GG669014.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD93, whole genome shotgun sequence\n+AATTTTTCTTGGATGGCGCGGGACAGAATCGAACTGCCGACACATGGAGCTTCAATCCATTGCTCTACCAACTGAGCTAC\n+CGAGCCAAAAACGGTCTGGACGGGACTCGAACCCGCGACCTCCTGCGTGACAGGCAGGCATTCTAACCAGCTGAACTACC\n+AAACCAATTCGTTTTTGCTTTATGCAAATGTATGCTTTAAAAAAT\n+>NZ_GG669013.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD92, whole genome shotgun sequence\n+GGAGGATTACCCAAGTCCGGCTGAAGGGAACGGTCTTGAAAACCGTCAGGCGGGTAAAACCGTGCAAGGGTTCGAATCCC\n+TTATCCTCCTTTCTTAGGAATCAATTTTCCNTGGTCTAATTATCGCGGGGTGGAGCAGTCAGGTAGCTCGTCGGGCTCAT\n+AACCCGAAGGTCGTAGGTTCAAATCCTGCCCCCGCAATTGCTTTT\n+>NZ_GG669012.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD91, whole genome shotgun sequence\n+GGAGTCTGACGAAGCTTATAAGCAGTTTATTGATGAGTATTTTCCATCTTACGACTATGCAAAAGTCAATCGTCTATTGC\n+AATTACGAGCAGACATTTTTTCTACTCTTGCAGGTGAAGCAATCGCAAGCGACGTTAACGGTAAATTTAATAACGACTTA\n+GAAAACATTACAAAACGAATCTACAATTCTAATTCTAATGCGTTGATG\n+>NZ_GG669011.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD90, whole genome shotgun sequence\n+GGAATCAGATGAAGTTTATAAACAATTCATTGATGAATATTTTCCATCCTTTGACTATGCGAAAGTTAATCGCTTGTTAC\n+AATTACGAGCAGACATTTTTTCTACCATTGCAGGTGAAGCAATAGCTAGTGATGTTAACGGTAAATTTAATAACGACTTA\n+GAGAATATCACAAAACGAATCTACAATTCTAATTCTAATGCGTTGATA\n+>NZ_GG669010.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD89, whole genome shotgun sequence\n+GTCGTATTTTTCACGAATAAAGATATCTGCATTTTCGTATTTTTCAGCTTTCCATGGTTCGATATTGCTCGCCCATAATT\n+GCCAACCTTCCTTGGTTTCAACAGGTTCTAACAAACGAAAAGCAACACCGCAAGCACCTTGAAACCGAGCTGTGTCAGAA\n+TCAAGCATGGCAAACCGCATATCATTCACTAACTCTGTCAGCCGTTCGAACTCTTT\n+>NZ_GG669009.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD88, whole genome shotgun sequence\n+CGCCAATGAAACATTAACCGCCGTAGCGAAAAACGCCAGCGGTACAGAAAGTACGCCAACAACGTTCCAAACGCCAGCGG\n+ATGAGACAACCGTAACCGCACCAACAATCACAGGAGTGACAGGTAATTCAACGGCAGGTTACGAGGTTAAAGGAACTACT\n+GATGCCAATGCCACGGTTGAGATCCGAAATGCAGGAGGTGCCGTGATAGGCACAGGGAGCGCC\n+>NZ_GG669008.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD87, whole genome shotgun sequence\n+CAGGATAGTATTTTCAGATGTATTCCCTGGTGTAGAAATAAAATCAGGTGATGGCGCTATGAATTTGTGGAGTTTGAACG\n+GTGGGTACAATAATTATTTAGCGACATCCCCAACAGGAACAGCTACAGGTTTTGGTGCAGACATTATTATCATTGATGAT\n+TTAATTAAAAATGCCGAAGAAGCAAATAATGCTATGGTTTTAGAGAAGCACTGGGATTGGTTTACC\n+>NZ_GG669007.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD86, whole genome shotgun sequence\n+GTATTTTTCATTTGCAACTATCCTTTTATTTTTTATTTGTATCAGTATCAATTTTACAGTAAACATGCATTTATGCCGAG\n+AAAATTTATTGATGTTGAGAAGAACCCTTAACTAAACTTGGAGACGAATGTCGGCATAGCGTGAGCTATTAAGCCGACCA\n+TTCGACAAGTTTTGGGATTGTTAAGGGTTCCGAGGCTCAACGTCAATAAAGCAATTGGAATAAAGCAAT\n+>NZ_GG669006.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD85, whole genome shotgun sequence\n+ATCAACTTTTCATAGTTCTTCTCAATATACTTACGGTACTTCTCTTGGTCTCGTTTGCTAAAATCTTCTAGCATCTCACT\n+TTGAGTAATACCGTGTAAATCAGCTTGTGCCAATAACTGTCTTTGAATTTTAACTAAAGCACGTTCGAAAACAGATTCTA\n+GTTCACTAAGAGTTTTCTTTTCCAGTTTCAAGCGTGCTTTGTCTTCTAATTCACGACGTTTTTCCCAGTA\n+>NZ_GG669005.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOLD84, whole genome shotgun sequence\n+TGGCAAAAGGTGCCGATTTTATTGGTGGCGTGGATCCTTATTCACTAGATGGTGATTACAAAAAATCATTGGCTGAAACA\n+TTCCGCTTAGCAGATAAACATGGTGTCGGTGTGGATATTCATTTACATGACCGTCATGAAGCTGGGACAACAACGATTAA\n+AGAAATTATTCGTTTAACGAAAGAATATGGTCTACAAGACAAAGTATTTATCAGTCATGCCTTCGGGTTAAA\n+>NZ_GG669004.1 Enterococcus faecalis TX0104 genomic scaffold SCAFFOL'..b'GTGGTATTACCCAAGTTACATTTTGTGTTACTGGAGAAACCCAACTTAAAATCTGTTACTAAATA\n+AGCCACACTAGACATTACAGCAGGACATAACAAAAATGGAATAAATAAAATAGGATTTAATACAGTAGGTAATCCATACA\n+TTACTGGTTCACCAATATTAAACAAAACAGGCATAATTCCAAGTTTTGCAACTTCTTTATAATGACTATTTTTTGATACC\n+CAAAAAATCGCAATTAATAAACCTAAAGTTGCATACCAGACAAACGATCCGTATGATACACTTGTCCAAACATAAGGAAT\n+AGTTTCATTGTTTTGATAAGCTTCTAAATTAACTAAAAGCGCTACTCCAAATACACCTTCCATAATAGGTGCCATAACAT\n+TTCCACCATGAATACCGAAAAACCAGAAAAATTGAACTAAGAAAGCAACTAATATAACAACAAAAAAACTTTGGGAAAGT\n+CCTAACATAGGGCGTTGTAATATTTCGTAAATTACATCTGTTAAAATTTTTCCTGTAATTCTATTTAACAAAAATGTCAA\n+AATAGCAATTATATAAAGAGAAACTAAAGCCGGAATAATTGATAAAAATGGTTTAGCGATAGCTGGAGGAACTGTATCAG\n+GTAATTTAATTGTCCAATTTTTATTCATGAGTTTACAAAAAATAATTGAAGATAAAAAACCTATGATTATTGCGGTAAAA\n+TAACCATTTGAATTAATTTGTGTACCAGGCAACAATCCTGATATAGTCACATTTAAACTGTTACCTGTAACTGTTATTCC\n+CTCAACATCAGTAAATAGTGTTGTTAAGTCAATATTATTATTATTCGATAAATTATAAGTTGAAGTCATAGAATTACTTA\n+TAGAAATAATAAATGAAGACAGGGCGACTAGTCCTGAAGACAAAGTATCTGTTTTATATATTTTAGCAATATTTACTCCT\n+AAACAATAAATAAACAGTAAGGAAACAATAGAAATGCTTCCTTTTGATATCAAATTATTTATATCTACTAACCATTGAAA\n+ATAATCAGTAATCTTCTCATAGCCAAATTGCATAGGAAAATCTACTAAAAAAGCATTTAATAATATTGCAACCGAACCTG\n+TCATTATTACAGGCATCGTACCCATAAATGAATCTCTTAACGCTACTAAAAATCGTTGATTCCCAATCTTAGTAGCTATA\n+GGTAAAACTTTATTCTGGATTGTATTCATTATTTTCTCACTCATTATGATTGACTCCTTCAAAAAATAGTTAGAAAGCGC\n+TATCTAATTATAGTATAGATTTTTTTGACCATTTGAACATGATAATCTATACTTAAAACATGGTATTTTCTTCATAGTTA\n+GTTCTATAAAGGAGGATAATAATGGAGGATTTTTGGTATCATAATAAGTCAGTTTCTGCTCCAATTTCCCTTTCCCAATG\n+CGGATATGAATCTTATCATCCCAATTCTTCTATTCGTAATTATATAGTTCAACAAAAATGGATATTTCATTATGTTTTAT\n+CTGGTAAGGGATTCTTAGAAGTAGAAGCTCAACATTTTGAACTTATAGAACACGATATTTTCTTTTTTTTCAAGGTCAAA\n+AAGTGAAGTATTATACAGATAAAAAGGAACCTTGGACACTGATTTGGTTAGGTATACAAGGTGATAAGACTTCTGAATTT\n+TTGAAAGAAACAACTTTACTAAATACTCATACAGTTAGCTTGACTAAGAATATAAATAAAAAACACACTATTGAAAATAG\n+TATGTGAAAATAGAGAACTAATTGGGGTTTGTCAACTAAACTGTGGAAGTTAAATAGTTAAGAGTTTTTAACCACCATAA\n+TTCTCTCGGCTATTTTGAAATCAGATAAATTTTGATCGGACACATAGTTGAATAAACCTACCGTTGTTACGGAAGGTAAA\n+TCGCATACTTTTCATTCTAGAGGAGAAGGTCTCGTTGATCATTAACTGCTTAAGCACCATAGCCCAGTTTTGAATTCGAC\n+CACCTGACCACTTCGCGTGTAATTCTTTCGTGCGTAAATAAAGTAGTTTTAGGAGTGCATTCTCATTAGAGAACGCTCCT\n+TTTTTTGTGACTTTTCTGAAGCTGGAGTGGACACTTTCAACCGCATTGGTAGTGTACATAATTTTTCGAATGGCACTACC\n+ATAATCAAATAGTTGTTCAACATGTGCAAAGTTCCGTTTCCAGACATCTACAGCACCAGAATAATGAGACCACCGATTTT\n+GAAAACTGCCAAAAGCAGCATGTGCAGCGTTTAGAGAAGAAGCACCGTAGAACTTTTTCATATCTCGGCAGACTTCCTTA\n+TAGTCCTTACTTGGAATATAGCGCAATGCATTTCGAACAAGATGAACAATACAGCGCTGAACAATTACCGATGGAAAGAT\n+CGCTTTTGCGCCTTCTTCGAGGCCAGAAACACCGTCCATCGAAATGAAAAAGACATCTTCGACACCACGTGCTTTCAGTT\n+CATCAAATACTTGCATCCAGCGATTTTTAGATTCTGTTTGATTTAACCATAATCCTAAAATCTCCTTATTTCCTTTGAGA\n+TCATAGCCAAGAATGGTGTATACAGCATATTCTTTGGCTTCATAATTTTCTCGTAAAGTAACATACATACAATCAACGAA\n+TAGAAAGGCATAACACTTTGCTAGGGGGCGGGCTTGCCATTCTTCCAATTCAGGAAGGACAGCGTCAGTGATATCTGAAA\n+TCATTTCATGGGAAATATCAAAGCCATAGATAGCTTCGACGGTTGCGGCAATATCTCGTTGACTCATTCCTCGTGCATAC\n+ATGGAAAGAACCTTCCCTTCGATGTCGGAGACATCTCGTTTTCTCTTAGGAATTAACTCTGGTTCAAAGGAAGCTTCCCG\n+GTCTCTAGGAACATCAATAGCTACTTCACCAAAACTGGTTTTAAGCGTTTTAGTTCCATAGCCATTTCGACGGTTATCGT\n+GTTCCTTAGGCTCTTTAGAATGGGCATCATAACCTAAATGATTATTCAATTCTCCTTGAAGCATTTTTTCAAAAAGGGGC\n+CCAAACACATCTTTCAAAGCATCTTGCATGTCATCGACAGATTCAGGTTGATAGGCATTCAGAATGGATTCAGCTAACTT\n+TTCGGCATCAGGATTTCTTTTCTTTCTAGCCATCGTGTAATCACCTCTTGATCTTATTGTAGAAAAAGAAAAACCGCGAA\n+GCAACCACCTGCCTAGGATTAATGGTTACTTACACGGTTTACATTACACTCTCATCATTAAAAAATATCTTTCGATATTA\n+CTAAAAAATGAAATTATCTATTTGAAATTTAAATCTGATAATATATTGAGTGTTCCAATGAGGGCTTTGATCCTATTATC\n+CATATCTTTTTCAGTTTTAATATTGATACACATTATAAGAAAAAGAAACTTTTGGTTAATTTATTTCATCCCAGTGCAAA\n+ATATAAAAAAGTAAAATAGACCATAGGCAATAGATTAACAATTAATATAATACAAGCAAATATTCTATTCATTGTATTTC\n+TGCTTTCAAAAAGTTCTAATATTGAAAGTATAATTCCACAAATGCCTATAATAAGTATGGGAATAAGATTAGAAAATAAC\n+ACCCCGAGCCAATCTGTGAAAATTACTATATTTACTAATATCCCTATTAACATACCTATCATATTTATTAAATCAATTTT\n+TTTCATTAGATATTTCTCCTTTATTAAATCTGAAGTACTTATATTAAAATAATTCTAAACTATTTACCTCAAAAAGTGCA\n+ATAAATTATTTCTGAACAATAAAATGATAGTCAAAACAAAAAAATATTGTTAATCGTTCAGAGCCATCCACCATTTTTAC\n+AATTAATGTATTCATATAAACTATTTACGATACTATAATAAAAGCATTATAGTTATTTATAAATAATTAAAGCAACT\n' |