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
<fastx_command> -h will display the help screen for that command.
Eg: fastx_trimmer -h
Note: When using fastx tools with Illumina HiSeq data from Casava 1.8, 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.
