swMATH ID: 17090
Software Authors: Hannon laboratory
Description: 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: Blat, SHRiMP, LastZ, 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
Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
Related Software: VarScan; Trimmomatic; Samtools; GATK; MethylCoder; mrsFAST; Bowtie 2; BSMAP; Bismark; BSmooth; BS Seeker; Cutadapt; FastQC; Pfam; MapSplice; eSNV-detect; Strelka; HaploReg; Salmon; ZOOM
Cited in: 2 Publications

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