Skip to content

Commit

Permalink
Merge pull request #1494 from lparsons/quast
Browse files Browse the repository at this point in the history 
Update Quast to version 4.5
  • Loading branch information
@bgruening
bgruening authored Sep 29, 2017
2 parents a548ae2 + 892e649 commit cd130fc
Show file tree
Hide file tree
Showing 5 changed files with 229 additions and 4 deletions.
24 changes: 20 additions & 4 deletions tools/quast/quast.xml
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<tool id="quast" name="Quast" version="4.1.1" >
<tool id="quast" name="Quast" version="4.5" >
<description>Genome assembly Quality</description>
<requirements>
<requirement type="package" version="4.1">quast</requirement>
<requirement type="package" version="4.5">quast</requirement>
</requirements>
<stdio>
<regex match="ERROR! exception caught!"
Expand All @@ -13,6 +13,7 @@
<![CDATA[
#import re
quast
--threads \${GALAXY_SLOTS:-4}
-o outputdir
#if $gene_selection == "eukaryote":
--eukaryote
Expand All @@ -34,7 +35,7 @@
--min-contig $min_contig
-l
#set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ])
$names
--contig-thresholds $threshold_contig
#for $k in $files:
Expand All @@ -48,7 +49,7 @@
mv outputdir/report.tsv '$quast_tsv' &&
mv outputdir/report.tex '$quast_tex' &&
mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' &&
mv outputdir/report.html '$report_html'
mv outputdir/report.html '$report_html'
]]>
</command>
<inputs>
Expand Down Expand Up @@ -91,6 +92,21 @@
<param name="gene_selection" value="prokaryotes"/>
<output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/>
</test>
<test>
<param name="input" value="contigs_1.fasta"/>
<param name="input.type_file" value="contig"/>
<param name="input_ref" value="NC000913.3_1-6650.fasta"/>
<param name="gene_selection" value="prokaryotes"/>
<output name="quast_tsv" file="Quast_report_withref.tsv" lines_diff="4"/>
</test>
<test>
<param name="input" value="contigs_1.fasta"/>
<param name="input.type_file" value="contig"/>
<param name="input_ref" value="NC000913.3_1-6650.fasta"/>
<param name="annot" value="NC000913.3_1-6650.gff"/>
<param name="gene_selection" value="prokaryotes"/>
<output name="quast_tsv" file="Quast_report_withref_withgenes.tsv" lines_diff="4"/>
</test>
</tests>
<help>
<![CDATA[
Expand Down
112 changes: 112 additions & 0 deletions tools/quast/test-data/NC000913.3_1-6650.fasta
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,112 @@
>NC_000913.3:1-6650
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTC
TGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGG
TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTAC
ACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAGGT
AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTG
GCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAA
CGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCG
CAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATT
AGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAA
ATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATC
GATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCA
GGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGAC
TACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGAC
GTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCG
ATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGC
ACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCT
CAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATG
GTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTG
ATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTG
CGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAG
CCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACC
TTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTC
GCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTG
TTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAA
AGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCT
CTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCC
AAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAAC
CCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTG
CGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAAC
GTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAA
TTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGAC
GAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCG
GACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGT
GAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAG
TTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAAT
ATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTG
TTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTG
CCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCT
GATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGACATGGTTAAAGTTTATGCCCC
GGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGT
TGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCA
GTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGA
AAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCT
GATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAT
GGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTT
TCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGG
GTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCT
GGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAA
AGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCA
GGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTT
CGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTA
CCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGT
ACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCC
GGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGC
GAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGT
GCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCT
GGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACA
AATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGA
TACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAA
TATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGC
GTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACAT
CAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAGGA
GACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGG
TCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAA
CGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTT
CCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCAC
GCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGT
AGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCAC
CGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCT
GCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGA
TTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATG
ACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGA
ATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATA
AAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGT
CGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGAT
AGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTG
GTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACA
TCACCGCTAAATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTG
GCGCGTCTTATCAGGCCTACGTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGG
CAGGATAAGGCGTTCACGCCGCATCCGGCATTGACTGCAAACTTAACGCTGCTCGTAGCG
TTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCAAAGAAGTAACCTTCGCTATT
AAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAACGACTCATCAG
ACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTC
ATCTGACGCCAGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTT
GTTGGTGATGATATCTCCCCAGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACG
GATCCCCATTTCCAGACGATAAGGCTGCATTAAATCGAGCGGGCGGAGTACGCCATACAA
GCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAATCGTCTTCGCTGAAGGTTTC
GGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGCGGGCATTCGC
CGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAA
CTGCTGGGAATTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTG
GTAATCAAGCGTTTTCGCAGGTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATT
TATGCCGACTTTAGCAAAAAATGAGAATGAGTTGATCGATAGTTGTGATTACTCCTGCGA
AACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATATCCGGATAACGCAATGGATC
AAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
22 changes: 22 additions & 0 deletions tools/quast/test-data/NC000913.3_1-6650.gff
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ASM584v2
#!genome-build-accession NCBI_Assembly:GCF_000005845.2
##sequence-region NC_000913.3 1 4641652
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=511145
NC_000913.3 RefSeq region 1 4641652 . + . ID=id0;Dbxref=taxon:511145;Is_circular=true;Name=ANONYMOUS;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=K-12;substrain=MG1655
NC_000913.3 RefSeq gene 190 255 . + . ID=gene0;Dbxref=EcoGene:EG11277,GeneID:944742;Name=thrL;gbkey=Gene;gene=thrL;gene_biotype=protein_coding;gene_synonym=ECK0001,JW4367;locus_tag=b0001
NC_000913.3 RefSeq CDS 190 255 . + 0 ID=cds0;Parent=gene0;Dbxref=ASAP:ABE-0000006,UniProtKB/Swiss-Prot:P0AD86,Genbank:NP_414542.1,EcoGene:EG11277,GeneID:944742;Name=NP_414542.1;Ontology_term=GO:0009088;gbkey=CDS;gene=thrL;go_process=threonine biosynthetic process|0009088||;product=thr operon leader peptide;protein_id=NP_414542.1;transl_table=11
NC_000913.3 RefSeq gene 337 2799 . + . ID=gene1;Dbxref=EcoGene:EG10998,GeneID:945803;Name=thrA;gbkey=Gene;gene=thrA;gene_biotype=protein_coding;gene_synonym=ECK0002,Hs,JW0001,thrA1,thrA2,thrD;locus_tag=b0002
NC_000913.3 RefSeq CDS 337 2799 . + 0 ID=cds1;Parent=gene1;Dbxref=ASAP:ABE-0000008,UniProtKB/Swiss-Prot:P00561,Genbank:NP_414543.1,EcoGene:EG10998,GeneID:945803;Name=NP_414543.1;Note=bifunctional: aspartokinase I (N-terminal)%3B homoserine dehydrogenase I (C-terminal);Ontology_term=GO:0005737,GO:0009088,GO:0009086,GO:0009090;experiment=N-terminus verified by Edman degradation: PMID 354697%2C4562989;gbkey=CDS;gene=thrA;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||,methionine biosynthetic process|0009086||,homoserine biosynthetic process|0009090||;product=Bifunctional aspartokinase/homoserine dehydrogenase 1;protein_id=NP_414543.1;transl_table=11
NC_000913.3 RefSeq gene 2801 3733 . + . ID=gene2;Dbxref=EcoGene:EG10999,GeneID:947498;Name=thrB;gbkey=Gene;gene=thrB;gene_biotype=protein_coding;gene_synonym=ECK0003,JW0002;locus_tag=b0003
NC_000913.3 RefSeq CDS 2801 3733 . + 0 ID=cds2;Parent=gene2;Dbxref=ASAP:ABE-0000010,UniProtKB/Swiss-Prot:P00547,Genbank:NP_414544.1,EcoGene:EG10999,GeneID:947498;Name=NP_414544.1;Ontology_term=GO:0005737,GO:0009088;gbkey=CDS;gene=thrB;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=homoserine kinase;protein_id=NP_414544.1;transl_table=11
NC_000913.3 RefSeq gene 3734 5020 . + . ID=gene3;Dbxref=EcoGene:EG11000,GeneID:945198;Name=thrC;gbkey=Gene;gene=thrC;gene_biotype=protein_coding;gene_synonym=ECK0004,JW0003;locus_tag=b0004
NC_000913.3 RefSeq CDS 3734 5020 . + 0 ID=cds3;Parent=gene3;Dbxref=ASAP:ABE-0000012,UniProtKB/Swiss-Prot:P00934,Genbank:NP_414545.1,EcoGene:EG11000,GeneID:945198;Name=NP_414545.1;Ontology_term=GO:0005737,GO:0009088;experiment=N-terminus verified by Edman degradation: PMID 9298646%2C9600841%2C9740056;gbkey=CDS;gene=thrC;go_component=cytoplasm|0005737||;go_process=threonine biosynthetic process|0009088||;product=L-threonine synthase;protein_id=NP_414545.1;transl_table=11
NC_000913.3 RefSeq gene 5234 5530 . + . ID=gene4;Dbxref=EcoGene:EG14384,GeneID:944747;Name=yaaX;gbkey=Gene;gene=yaaX;gene_biotype=protein_coding;gene_synonym=ECK0005,JW0004;locus_tag=b0005
NC_000913.3 RefSeq CDS 5234 5530 . + 0 ID=cds4;Parent=gene4;Dbxref=ASAP:ABE-0000015,UniProtKB/Swiss-Prot:P75616,Genbank:NP_414546.1,EcoGene:EG14384,GeneID:944747;Name=NP_414546.1;gbkey=CDS;gene=yaaX;product=DUF2502 family putative periplasmic protein;protein_id=NP_414546.1;transl_table=11
NC_000913.3 RefSeq repeat_region 5565 5669 . + . ID=id1;Note=RIP1 (repetitive extragenic palindromic) element%3B contains 2 REP sequences and 1 IHF site;gbkey=repeat_region
NC_000913.3 RefSeq gene 5683 6459 . - . ID=gene5;Dbxref=EcoGene:EG10011,GeneID:944749;Name=yaaA;gbkey=Gene;gene=yaaA;gene_biotype=protein_coding;gene_synonym=ECK0006,JW0005;locus_tag=b0006
NC_000913.3 RefSeq CDS 5683 6459 . - 0 ID=cds5;Parent=gene5;Dbxref=ASAP:ABE-0000018,UniProtKB/Swiss-Prot:P0A8I3,Genbank:NP_414547.1,EcoGene:EG10011,GeneID:944749;Name=NP_414547.1;gbkey=CDS;gene=yaaA;product=peroxide resistance protein%2C lowers intracellular iron;protein_id=NP_414547.1;transl_table=11
###
37 changes: 37 additions & 0 deletions tools/quast/test-data/Quast_report_withref.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
Assembly contigs_1_fasta
# contigs (>= 0 bp) 3
# contigs (>= 1000 bp) 3
Total length (>= 0 bp) 6710
Total length (>= 1000 bp) 6710
# contigs 3
Largest contig 3980
Total length 6710
Reference length 6650
GC (%) 51.28
Reference GC (%) 52.00
N50 3980
NG50 3980
N75 1610
NG75 1610
L50 1
LG50 1
L75 2
LG75 2
# misassemblies 0
# misassembled contigs 0
Misassembled contigs length 0
# local misassemblies 0
# unaligned mis. contigs 0
# unaligned contigs 0 + 1 part
Unaligned length 1950
Genome fraction (%) 71.579
Duplication ratio 1.000
# N's per 100 kbp 0.00
# mismatches per 100 kbp 0.00
# indels per 100 kbp 0.00
Largest alignment 2030
Total aligned length 4760
NA50 1610
NGA50 1610
LA50 2
LGA50 2
38 changes: 38 additions & 0 deletions tools/quast/test-data/Quast_report_withref_withgenes.tsv
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
Assembly contigs_1_fasta
# contigs (>= 0 bp) 3
# contigs (>= 1000 bp) 3
Total length (>= 0 bp) 6710
Total length (>= 1000 bp) 6710
# contigs 3
Largest contig 3980
Total length 6710
Reference length 6650
GC (%) 51.28
Reference GC (%) 52.00
N50 3980
NG50 3980
N75 1610
NG75 1610
L50 1
LG50 1
L75 2
LG75 2
# misassemblies 0
# misassembled contigs 0
Misassembled contigs length 0
# local misassemblies 0
# unaligned mis. contigs 0
# unaligned contigs 0 + 1 part
Unaligned length 1950
Genome fraction (%) 71.579
Duplication ratio 1.000
# N's per 100 kbp 0.00
# mismatches per 100 kbp 0.00
# indels per 100 kbp 0.00
# genes 3 + 3 part
Largest alignment 2030
Total aligned length 4760
NA50 1610
NGA50 1610
LA50 2
LGA50 2

0 comments on commit cd130fc

Please sign in to comment.