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. Example of such mapping programs are:
- MAQ and many many others
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.