FastX toolkit

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Remove contaminant adapter sequences from your reads prior to other NGS processing

SimilarTo.png: cutadapt , seq_crumbs , PrinSeq, Trimmomatic

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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 and was also included in Galaxy.

You can find more information about FastX toolkit in the web site[1].

FASTQ-to-FASTA converter Convert FASTQ files to FASTA files.
FASTQ Information Chart Quality Statistics and Nucleotide Distribution
FASTQ/A Collapser Collapsing identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)
FASTQ/A Trimmer Shortening reads in a FASTQ or FASTQ files (removing barcodes or noise).
FASTQ/A Renamer Renames the sequence identifiers in FASTQ/A file.
FASTQ/A Clipper Removing sequencing adapters / linkers
FASTQ/A Reverse-Complement Producing the Reverse-complement of each sequence in a FASTQ/FASTA file.
FASTQ/A Barcode splitter Splitting a FASTQ/FASTA files containning multiple samples
FASTA Formatter changes the width of sequences line in a FASTA file
FASTA Nucleotide Changer Convets FASTA sequences from/to RNA/DNA
FASTQ Quality Filter Filters sequences based on quality
FASTQ Quality Trimmer Trims (cuts) sequences based on quality
FASTQ Masker Masks nucleotides with 'N' (or other character) based on quality


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