ReadStackCorrector is a software to correct substitution sequencing errors in experiments with deep coverage, specifically intended for Illumina sequencing reads. It is released under Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) as a Free and Open Source Software Project.

More details about ReadStackCorrector you can get under: https://github.com/ice91/ReadStackCorrector

requirement: hadoop cluster

step 1: convert *.fastq to *.sfq

e.g. java Fastq2Sfq Ecoli.fastq Ecoli.sfq

step 2: upload *.sfq to HDFS

e.g. hadoop fs -put Ecoli.sfq Ecoli

step 3: exceute the ReadStackCorrector

e.g. hadoop jar ReadStackCorrector.jar -in Ecoli -out Ecoli_ec

step 4: download *.fastq from HDFS

e.g. hadoop fs -cat Ecoli_ec_file/* > Ecoli_ec.fastq

(You can use CloudBrush as postprocessor to do the de novo assembly)

e.g. hadoop jar CloudBrush.jar -reads Ecoli_ec -asm Ecoli_ec_Brush -k 21 -readlen 36

More details about CloudBrush Project you can get under: https://github.com/ice91/CloudBrush