Nesoni --

"Swiss army knife for NGS SNP calling / RNA-Seq DGE / read cleaning. A high-throughput sequencing data analysis toolset, focussing on analysis of short reads aligned to a reference sequence." acceding to the authors.

The software and instructions can be found on: ​http://bioinformatics.net.au/software.nesoni.shtml or by simply typing nesoni at the prompt once logged in on my-mgrid.

The program has a very good adopter clipping and quality trimming function called clip.

Mykopat Grid specifics

Sample usage for clipping an Illumina dataset:

qsub -l h_rt=4:0:0,h_vmem=1G -cwd -N nesoni -m ae <<< 'nesoni clip --quality 30 --length 35 --trim-start 3 --trim-end 5 --gzip yes s7_trimmed pairs: s_7_1_sequence.txt.gz s_7_2_sequence.txt.gz'