ECHO
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Description
ECHO is an error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina's Genome Analyzer II. The algorithm uses a Bayesian framework to improve the quality of the reads in a given data set by employing maximum a posteriori estimation.
License
BSD license
Use
{{module_avail_add|name=echo} } Example of shell script:
#!/bin/bash #PBS -N myecho #PBS -l nodes=1:ppn=8 #PBS -l mem=10g #PBS -j oe # let's initialize modules . /packages/run/modules-2.0/init/sh trap "clean_scratch" TERM EXIT module add echo-1.12 # let's set the necessary variables DATADIR="/storage/brno2/home/$LOGNAME/" # let's copy the input data cp -r $DATADIR/100000.fastq $SCRATCHDIR # let's change the working directory cd $SCRATCHDIR # let's perform the computation ECHO -k 15 -u $PBS_NUM_PPN -b 300000 --nh 256 -o 1k-fixed 100000.fastq # let's copy-out the result cp 1k-fixed $DATADIR || export CLEAN_SCRATCH=false
Documentation
http://uc-echo.sourceforge.net/README.txt