Mercurial > repos > edward-kirton > phrap
comparison 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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| -1:000000000000 | 0:f9e4e6fe0e73 |
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| 1 <tool id="phrap" name="Phrap" version="1.0.0"> | |
| 2 <description>Assemble long reads/short contigs</description> | |
| 3 <command interpreter='bash'>phrap_wrapper.sh $label $fasta_infile $qual_infile $fasta_outfile $qual_outfile $singlets_outfile $fasta_outfile.extra_files_path</command> | |
| 4 | |
| 5 <inputs> | |
| 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, ..." /> | |
| 7 <param name="fasta_infile" type="data" format="fasta" label="Long reads or contig sequences" /> | |
| 8 <param name="qual_infile" type="data" format="qual" optional='True' label="Optional sequence quality scores (Phred-scaled)" /> | |
| 9 </inputs> | |
| 10 | |
| 11 <outputs> | |
| 12 <data name="fasta_outfile" format="fasta" /> | |
| 13 <data name="qual_outfile" format="qual" label="Contig quality scores" /> | |
| 14 <data name="singlets_outfile" format="fasta" label="Singlets Fasta" /> | |
| 15 </outputs> | |
| 16 | |
| 17 <help> | |
| 18 **What it does** | |
| 19 | |
| 20 phrap ("phragment assembly program", or "phil's revised assembly | |
| 21 program"; a homonym of "frappe" = French for "swat") -- a | |
| 22 program for assembling shotgun DNA sequence data. Key features: | |
| 23 allows use of entire read (not just trimmed high quality part); uses a | |
| 24 combination of user-supplied and internally computed data quality | |
| 25 information to improve accuracy of assembly in the presence of | |
| 26 repeats; constructs contig sequence as a mosaic of the highest quality | |
| 27 parts of reads (rather than a consensus); provides extensive information | |
| 28 about assembly (including quality values for contig sequence) to | |
| 29 assist trouble-shooting; able to handle very large datasets. | |
| 30 | |
| 31 **Notes** | |
| 32 | |
| 33 phrap is great for assembling Sanger shotgun reads but should not be used for next-generation data (e.g. Illumina, Solid, 454, etc.). | |
| 34 However phrap is useful for combining short-read assemblies from Velvet or Abyss (i.e. results from using multiple k-mer parameters). | |
| 35 When used for this purpose, you should filter out short sequences first (e.g. less than 200-1000bp, depending on number of contigs). | |
| 36 | |
| 37 **Reference** | |
| 38 | |
| 39 http://www.phrap.org/phredphrap/phrap.html | |
| 40 </help> | |
| 41 </tool> |