Quality control

Quality control & raw data processing tools

FastqMcf (ea-utils)

https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md

Trim Galore

- adapter removal and read quality trimming

- internally based on Cutadapt and FastQC

https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

FastQC

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

FASTX-Toolkit

http://hannonlab.cshl.edu/fastx_toolkit/

Usearch

http://www.drive5.com/usearch/manual/cmd_fastq_filter.html

Trimmomatic

http://www.usadellab.org/cms/?page=trimmomatic

Sickle

https://github.com/ucdavis-bioinformatics/sickle