FastX-Toolkit

A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

Homepage Version(s): 0.11.8

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FastX-Toolkit requires an environment module

In order to use FastX-Toolkit, you must first load the appropriate environment module:

module load gnu

From the developer's website:

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. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.

Usage on the HPC

# Load the 'gnu' environment module
$ module load gnu

$ fastx36 --help

$ fastq_to_fasta ...