- 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.'
- package fastx_toolkit¶
- depends gnuplot:
- depends libgcc-ng:
- depends libgtextutils:
- depends libstdcxx-ng:
- depends perl:
- depends perl-gd:
- depends perl-gdgraph-histogram:
- depends perl-perlio-gzip:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install fastx_toolkit and update with:: mamba update fastx_toolkit
To create a new environment, run:
mamba create --name myenvname fastx_toolkit
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/fastx_toolkit:<tag> (see `fastx_toolkit/tags`_ for valid values for ``<tag>``)