Mercurial > repos > iuc > quast
annotate quast.xml @ 5:81df4950d65b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
author | iuc |
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date | Tue, 04 Dec 2018 06:49:05 -0500 |
parents | 0834c823d4b9 |
children | f30d03867854 |
rev | line source |
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5
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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1 <tool id="quast" name="Quast" version="5.0.2" > |
0
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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2 <description>Genome assembly Quality</description> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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3 <requirements> |
5
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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4 <requirement type="package" version="5.0.2">quast</requirement> |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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5 </requirements> |
5
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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6 <command detect_errors="exit_code"> |
0
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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7 <![CDATA[ |
5
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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8 #import re |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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9 quast |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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10 --threads \${GALAXY_SLOTS:-4} |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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11 -o outputdir |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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12 #if $gene_selection == "eukaryote": |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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13 --eukaryote |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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14 #else if $gene_selection == "metagenes": |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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15 --meta |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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16 #end if |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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17 $large |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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18 #if $input_ref: |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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19 -R '$input_ref' |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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changeset
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20 #if $input_operon: |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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21 -O '$input_operon' |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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changeset
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22 #end if |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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23 #if $annot: |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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24 -g '$annot' |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
diff
changeset
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25 #end if |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
diff
changeset
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26 #end if |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
diff
changeset
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27 #if $input_size: |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
diff
changeset
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28 --est-ref-size $input_size |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
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changeset
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29 #end if |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
4
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changeset
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30 --min-contig $min_contig |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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31 -l |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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32 #set names = ','.join( [re.sub('[^\w\-_]', '_', str($x.element_identifier)) for $x in $input ]) |
3
6fcbee531de6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
iuc
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33 |
5
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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34 '$names' |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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35 --contig-thresholds $threshold_contig |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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36 #for $k in $input: |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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37 $k |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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38 #end for |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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39 && mkdir '$report_html.files_path' |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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40 && cp outputdir/*.html '$report_html.files_path' |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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41 #if str($input_ref): |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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42 && cp -R outputdir/icarus_viewers '$report_html.files_path' |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
parents:
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43 #end if |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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44 ]]> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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45 </command> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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46 <inputs> |
4
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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47 <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file" multiple="True"/> |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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48 <param name="type_file" type="select" label="Type of data"> |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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49 <option value="contig">Contig</option> |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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50 <option value="scaffold">Scaffold</option> |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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51 </param> |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
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52 <param name="input_size" type="integer" label="Size of reference genome" optional="True" argument="--est-ref-size" |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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53 help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/> |
5
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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54 <param argument="--large" type="boolean" truevalue="--large" falsevalue="" label="Run quast in --large mode for large genomes" help="Uses minimap2 aligner, improves transposable element handling and alignment thresholds"/> |
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0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
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55 <param name="input_ref" type="data" format="fasta" label="Reference genome" optional="True" argument="-R" |
0
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
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56 help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/> |
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0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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57 <param name="annot" type="data" format="gff, gff3, bed" label="Gene Annotations" optional="True" argument="-G" |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
parents:
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58 help="Gene coordinates for the reference genome (only relevant if the reference genome is used). "/> |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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59 <param name="input_operon" type="data" format="gff, gff3, bed" label="Operon Annotations" optional="True" argument="-O" help="Operon coordinates for the reference genome (only relevant if the reference genome is used)."/> |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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60 <param name="gene_selection" type="select" label="Type of organism"> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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61 <option value="prokaryotes">Prokaryotes</option> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
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62 <option value="eukaryote">Eukaryote</option> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
parents:
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63 </param> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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64 <param name="min_contig" type="integer" value="500" label="Lower Threshold" argument="--min-contig" |
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0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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65 help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account [default is 500]"/> |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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66 <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds" |
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0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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67 help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.[default is 0,1000]"/> |
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736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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68 </inputs> |
736d51130b41
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09
iuc
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69 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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70 <data format="txt" name="log_txt" label="Quast: Log" from_work_dir="outputdir/quast.log"/> |
81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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71 <data format="tabular" name="mis_ass_tsv" label="Quast: Misassemblies" from_work_dir="outputdir/contigs_reports/misassemblies_report.txt"> |
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0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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72 <filter>input_ref is not None</filter> |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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73 </data> |
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81df4950d65b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 600e99f5044018f7d0046b1bfdc6dc392c4e6baa
iuc
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74 <data format="tabular" name="unalign_tsv" label="Quast: Unaligned contigs" from_work_dir="outputdir/contigs_reports/unaligned_report.tsv"> |
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0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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75 <filter>input_ref is not None</filter> |
0834c823d4b9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 2c56b5f07500507dad503aab6ec0619ec37f8b87
iuc
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76 </data> |
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77 <data format="tabular" name="quast_tsv" label="Quast: Report (tabulal)" from_work_dir="outputdir/report.tsv"/> |
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78 <data format="html" name="report_html" label="Quast: Report (HTML)" from_work_dir="outputdir/report.html"/> |
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79 <data format="pdf" name="report_pdf" label="Quast: Report (PDF)" from_work_dir="outputdir/report.pdf"/> |
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80 </outputs> |
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81 <tests> |
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82 <test> |
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83 <!-- Test with reference and genes annotations --> |
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84 <param name="input" value="contigs2.fna,contigs1.fna"/> |
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85 <param name="input_ref" value="reference.fna"/> |
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86 <param name="type_file" value="contig"/> |
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87 <param name="annot" value="genes.gff"/> |
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88 <param name="gene_selection" value="prokaryotes"/> |
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89 <param name="large" value="true"/> |
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90 <output name="quast_tsv" file="test1_output.tsv" lines_diff="4"/> |
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91 </test> |
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92 <test> |
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93 <!-- Test without reference --> |
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94 <param name="input" value="contigs2.fna,contigs1.fna"/> |
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95 <param name="type_file" value="contig"/> |
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96 <output name="quast_tsv" file="test2_output.tsv" lines_diff="4"/> |
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97 <output name="report_html" file="test2_report.html" lines_diff="50"/> |
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98 <output name="report_pdf" file="test2_report.pdf" compare="sim_size"/> |
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99 </test> |
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100 </tests> |
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101 <help> |
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102 <![CDATA[ |
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103 **What it does** |
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104 |
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105 QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. |
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106 |
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107 If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.bioinf.spbau.ru/manual.html>`_. |
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108 |
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109 **Using Quast without reference** |
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110 |
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111 Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs: |
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112 |
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113 * Quast report in HTML format |
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114 * `Contig viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file) |
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115 * `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format |
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116 * Quast log (a file technical information about Quast tool execution) |
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117 |
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118 The **tab delimited Quast report** will contain the following information:: |
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119 |
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120 Assembly pit_fna cef_fna car_fna |
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121 # contigs (>= 0 bp) 100 91 94 |
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122 # contigs (>= 1000 bp) 62 58 61 |
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123 Total length (>= 0 bp) 6480635 6481216 6480271 |
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124 Total length (>= 1000 bp) 6466917 6468946 6467103 |
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125 # contigs 71 66 70 |
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126 Largest contig 848753 848766 662053 |
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127 Total length 6473173 6474698 6473810 |
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128 GC (%) 66.33 66.33 66.33 |
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129 N50 270269 289027 254671 |
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130 N75 136321 136321 146521 |
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131 L50 7 7 8 |
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132 L75 15 15 16 |
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133 # N's per 100 kbp 0.00 0.00 0.00 |
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134 |
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135 where values are defined as specified in `Quast manual <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ |
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136 |
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137 **Quast report in HTML format** contains graphs in addition to the above metrics, while **Contig viewer** draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see `--est-ref-size`), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel: |
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138 |
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139 .. image:: $PATH_TO_IMAGES/contig_view_noR.png |
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140 :width: 558 |
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141 :height: 412 |
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142 |
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143 Also see `Plot description <http://quast.bioinf.spbau.ru/manual.html#sec3.2>`_ section of the manual. |
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144 |
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145 **Using Quast with reference** |
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146 |
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147 Car, pit, and cef are in fact assemblies of *Pseudomonas aeruginosa* UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing *P. aeruginosa* pa14 genome to **Reference genome** input box). The following outputs will be produced (note the alignment viewer): |
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148 |
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149 * Quast report in HTML format |
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150 * `Contig viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file) |
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151 * `Alignment viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file) |
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152 * `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format |
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153 * Summary of `misassemblies <http://quast.bioinf.spbau.ru/manual.html#sec3.1.2>`_ |
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154 * Summary of `unaligned contigs <http://quast.bioinf.spbau.ru/manual.html#sec3.1.3>`_ |
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155 * Quast log (a file technical information about Quast tool execution) |
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156 |
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157 With the reference Quast produces a much more comprehensive set of results:: |
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158 |
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159 Assembly pit_fna cef_fna car_fna |
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160 # contigs (>= 0 bp) 100 91 94 |
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161 # contigs (>= 1000 bp) 62 58 61 |
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162 Total length (>= 0 bp) 6480635 6481216 6480271 |
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163 Total length (>= 1000 bp) 6466917 6468946 6467103 |
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164 # contigs 71 66 70 |
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165 Largest contig 848753 848766 662053 |
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166 Total length 6473173 6474698 6473810 |
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167 Reference length 6537648 6537648 6537648 |
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168 GC (%) 66.33 66.33 66.33 |
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169 Reference GC (%) 66.29 66.29 66.29 |
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170 N50 270269 289027 254671 |
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171 NG50 270269 289027 254671 |
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172 N75 136321 136321 146521 |
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173 NG75 136321 136321 136321 |
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174 L50 7 7 8 |
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175 LG50 7 7 8 |
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176 L75 15 15 16 |
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177 LG75 15 15 17 |
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178 # misassemblies 0 0 0 |
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179 # misassembled contigs 0 0 0 |
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180 Misassembled contigs length 0 0 0 |
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181 # local misassemblies 1 1 2 |
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182 # unaligned mis. contigs 0 0 0 |
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183 # unaligned contigs 0 + 0 0 + 0 0 + 0 |
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184 part part part |
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185 Unaligned length 0 0 0 |
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186 Genome fraction (%) 99.015 99.038 99.025 |
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187 Duplication ratio 1.000 1.000 1.000 |
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188 # N's per 100 kbp 0.00 0.00 0.00 |
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189 # mismatches per 100 kbp 3.82 3.63 3.49 |
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190 # indels per 100 kbp 1.19 1.13 1.13 |
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191 Largest alignment 848753 848766 662053 |
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192 Total aligned length 6473163 6474660 6473792 |
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193 NA50 270269 289027 254671 |
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194 NGA50 270269 289027 254671 |
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195 NA75 136321 136321 146521 |
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196 NGA75 136321 136321 136321 |
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197 LA50 7 7 8 |
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198 LGA50 7 7 8 |
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199 LA75 15 15 16 |
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200 LGA75 15 15 17 |
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201 |
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202 where, again, values are defined as specified in `Quast manual <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly. |
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203 |
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204 Using reference also produces an **Alignment viewer**: |
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205 |
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206 .. image:: $PATH_TO_IMAGES/Align_view.png |
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207 :width: 515 |
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208 :height: 395 |
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209 |
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210 Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_). |
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211 |
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212 ]]> |
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213 </help> |
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214 |
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215 <citations> |
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216 <citation type="bibtex">@ARTICLE{a1, |
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217 author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler}, |
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218 title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075} |
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219 }</citation> |
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220 <citation type="bibtex">@misc{quast41, |
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221 title = {{Quast} v4.1}, |
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222 howpublished = {http://bioinf.spbau.ru/quast}, |
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223 note = {Released May 2016}} |
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224 }</citation> |
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225 </citations> |
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226 </tool> |