recipe fastx_toolkit

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

https://github.com/agordon/fastx_toolkit

License

AGPL

Recipe

/fastx_toolkit/meta.yaml

package fastx_toolkit

(downloads) docker_fastx_toolkit

Versions

0.0.14-7, 0.0.14-6, 0.0.14-5, 0.0.14-4, 0.0.14-3, 0.0.14-2, 0.0.14-1, 0.0.14-0

Depends cython

Depends gnuplot

>=5.0.5

Depends libgcc-ng

>=4.9

Depends libgtextutils

Depends libstdcxx-ng

>=4.9

Depends perl

Depends perl-gd

Depends perl-gdgraph-histogram

Depends perl-perlio-gzip

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install fastx_toolkit

and update with:

conda update fastx_toolkit

or use the docker container:

docker pull quay.io/biocontainers/fastx_toolkit:<tag>

(see fastx_toolkit/tags for valid values for <tag>)