Filter paired end based on GC content

[Rhodotus]

Our genomic libraries (Arabidopsis) are contaminated with an endophytic bacteria and we would like to filter out this contaminant.

Is there any tool out there, which can filter paired reads based on GC content ?

I have not found many filtering tools respecting the paired end order. Trimmomatic was a very good one for other sorts of filters but lacks GC content option. Prinseq can filter after GC content but not in paired end ones. An alternative could be a tool selecting paired end reads from two unpaired files.

Cheers.

[maasha]

You can use Biopieces (www.biopieces.org) for this:

read_fastq -i in.fq | analyze_gc | grab -e 'GC% >= 65' | order_pairs | write_fastq -o out.fq -x

This solution works, but may feel slow since Biopieces don't assume that the order of entries are pre-sorted. A Perl hack will be faster (depending on how fast you are at writing and proofing the code).

[JackieBadger]

PRINSEQ

http://prinseq.sourceforge.net/manual.html