Autoskewer is a sequence adapter trimmer intended to robustly remove adapter contamination from fastq-formatted sequence data without prior knowledge of the contaminating adapter sequences.
Autoskewer is a wrapper for skewer, which actually performs the trimming.
Autoskewer depends on
- bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
- skewer http://github.com/relipmoc/skewer
- python 2.7
git clone http://github.com/wltrimbl/autoskewer
cd autoskewer
make
bowtie2, skewer, and the autoskewer/src directory must be in PATH.
autoskewer.py example/sample.fastq
Produces sample.fastq.P5.csv sample.fastq.P5.err sample.fastq.P7.csv sample.fastq.P7.err and the output sample.scrubbed.fastq
autoskewer.py
does not have any options at the moment.
Will Trimble and Wolfgang Gerlach at University of Chicago, Institute for Genomics and Systems Biology.