FastX toolkit
Remove contaminant adapter sequences from your reads prior to other NGS processing
: cutadapt , seq_crumbs , PrinSeq, Trimmomatic
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 |
References:
