Mercurial > repos > edward-kirton > phrap
annotate phrap/phrap.xml @ 0:f9e4e6fe0e73 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:41:56 -0400 |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="phrap" name="Phrap" version="1.0.0"> |
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2 <description>Assemble long reads/short contigs</description> |
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3 <command interpreter='bash'>phrap_wrapper.sh $label $fasta_infile $qual_infile $fasta_outfile $qual_outfile $singlets_outfile $fasta_outfile.extra_files_path</command> |
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4 |
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5 <inputs> |
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6 <param name="label" type="text" value="seqs" label="Label for naming contig sequences (e.g. library or sample name)" help="Contigs will be named LABEL.Contig1, ..." /> |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 <param name="fasta_infile" type="data" format="fasta" label="Long reads or contig sequences" /> |
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8 <param name="qual_infile" type="data" format="qual" optional='True' label="Optional sequence quality scores (Phred-scaled)" /> |
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9 </inputs> |
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10 |
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11 <outputs> |
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12 <data name="fasta_outfile" format="fasta" /> |
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13 <data name="qual_outfile" format="qual" label="Contig quality scores" /> |
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14 <data name="singlets_outfile" format="fasta" label="Singlets Fasta" /> |
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15 </outputs> |
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16 |
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17 <help> |
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18 **What it does** |
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19 |
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20 phrap ("phragment assembly program", or "phil's revised assembly |
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21 program"; a homonym of "frappe" = French for "swat") -- a |
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22 program for assembling shotgun DNA sequence data. Key features: |
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23 allows use of entire read (not just trimmed high quality part); uses a |
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24 combination of user-supplied and internally computed data quality |
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25 information to improve accuracy of assembly in the presence of |
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26 repeats; constructs contig sequence as a mosaic of the highest quality |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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27 parts of reads (rather than a consensus); provides extensive information |
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28 about assembly (including quality values for contig sequence) to |
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29 assist trouble-shooting; able to handle very large datasets. |
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30 |
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31 **Notes** |
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32 |
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33 phrap is great for assembling Sanger shotgun reads but should not be used for next-generation data (e.g. Illumina, Solid, 454, etc.). |
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34 However phrap is useful for combining short-read assemblies from Velvet or Abyss (i.e. results from using multiple k-mer parameters). |
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35 When used for this purpose, you should filter out short sequences first (e.g. less than 200-1000bp, depending on number of contigs). |
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36 |
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37 **Reference** |
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38 |
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39 http://www.phrap.org/phredphrap/phrap.html |
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40 </help> |
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41 </tool> |