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

Versions:

0.0.14-11,  0.0.14-10,  0.0.14-9,  0.0.14-8,  0.0.14-7,  0.0.14-6,  0.0.14-5,  0.0.14-4,  0.0.14-3, 

0.0.14-11,  0.0.14-10,  0.0.14-9,  0.0.14-8,  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:

• gnuplot >=5.0.5

• libgcc-ng >=12

• libgtextutils >=0.7,<0.8.0a0

• libstdcxx-ng >=12

• perl

• perl-gd

• perl-gdgraph-histogram

• perl-perlio-gzip

Required By:

• mintie

• rop

• pipits

• pispino

• plastid

• jaffa

Installation

With an activated Bioconda channel (see 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>)

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