view tools/ilmn_pacbio/quake.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="quake" name="Quake" version="1.0.0">
  <description>Quality-aware error correction</description>
  <command interpreter="python"> --default_cutoff=10 --headers -k $k -f $fofnfile -p 12 > $output1
    <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
    <configfile name="fofnfile">
    <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />

**What it does**

Applies the Quake_ algorithm for quality-aware correction of
substitution error in short reads.

Kelley DR, Schatz MC, Salzberg SL.
"Quake: quality-aware detection and correction of sequencing errors."
*Genome Biol.* 2010;11(11):R116.

.. _Quake:

**Parameter list**

    k-mer size for detecting spurious k-mers versus true k-mers from
    the genome.  Recommendations for choosing a value of k can be found

.. _here:


A FASTQ file of corrected and trimmed reads.