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.

Availability

Version 1.12

Licence

BSD license

Use

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

Program manager

meta@cesnet.cz

Homepage

http://uc-echo.sourceforge.net/