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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:41:56 -0400
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f9e4e6fe0e73 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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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
f9e4e6fe0e73 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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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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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>