The Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit
) is installed on fourierseq and it is a set of commandline tools for processing of fasta/fastq data files. It can be useful for any preprocessing of data, such as filtering by quality, base trimming etc.
For more usage information, check the documentation here
Note: When using fastx tools with Illumina HiSeq data, make sure to add -Q33 option. Fastx tools assumes quality scores with ASCII offset 64, but the data is Sanger encoded(offset 33), so this needs to be specified explicitly by adding the -Q33 flag.
