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FASTX Toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).  The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs.  However, it is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome – manipulating the sequences to produce better mapping results.

The FASTX-Toolkit tools perform some of these preprocessing tasks.


Usage on Bridges-2

To see what versions of ABySS are available and if there is more than one, which is the default, along with some help, type

module spider abyss

To use ABySS, include a command like this in your batch script or interactive session to load the ABySS module: (note ‘module load’ is case-sensitive):

module load ABySS

Usage on Bridges

To see what other modules are needed, what commands are available and how to get additional help type

module help fastx

To see what versions of FASTX are available type

module avail fastx

To use FASTX, include a command like this in your batch script or interative session to load the FASTX module:

module load fastx

Be sure you also load any other modules needed, as listed by the module help fastx command.