How To Install fastx_toolkit on Fedora 36
Introduction
In this tutorial we learn how to install fastx_toolkit on Fedora 36.
What is 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 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.
We can use yum or dnf to install fastx_toolkit on Fedora 36. In this tutorial we discuss both methods but you only need to choose one of method to install fastx_toolkit.
Install fastx_toolkit on Fedora 36 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
After updating yum database, We can install fastx_toolkit using dnf by running the following command:
sudo dnf -y install fastx_toolkit
Install fastx_toolkit on Fedora 36 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
After updating yum database, We can install fastx_toolkit using yum by running the following command:
sudo yum -y install fastx_toolkit
How To Uninstall fastx_toolkit on Fedora 36
To uninstall only the fastx_toolkit package we can use the following command:
sudo dnf remove fastx_toolkit
fastx_toolkit Package Contents on Fedora 36
/usr/bin/fasta_clipping_histogram.pl
/usr/bin/fasta_formatter
/usr/bin/fasta_nucleotide_changer
/usr/bin/fastq_masker
/usr/bin/fastq_quality_boxplot_graph.sh
/usr/bin/fastq_quality_converter
/usr/bin/fastq_quality_filter
/usr/bin/fastq_quality_trimmer
/usr/bin/fastq_to_fasta
/usr/bin/fastx_artifacts_filter
/usr/bin/fastx_barcode_splitter.pl
/usr/bin/fastx_clipper
/usr/bin/fastx_collapser
/usr/bin/fastx_nucleotide_distribution_graph.sh
/usr/bin/fastx_nucleotide_distribution_line_graph.sh
/usr/bin/fastx_quality_stats
/usr/bin/fastx_renamer
/usr/bin/fastx_reverse_complement
/usr/bin/fastx_trimmer
/usr/bin/fastx_uncollapser
/usr/lib/.build-id
/usr/lib/.build-id/12
/usr/lib/.build-id/12/7acd85d4b3988301026162616a5767b00aba73
/usr/lib/.build-id/14
/usr/lib/.build-id/14/4b35bc046e69cd36a77dcf6214aba6c44b3cfb
/usr/lib/.build-id/22
/usr/lib/.build-id/22/0d069f389b611784ab6dbb892006bec06282c6
/usr/lib/.build-id/37
/usr/lib/.build-id/37/51917a921cf96e4ab1e5503017bafa7f9898fa
/usr/lib/.build-id/49
/usr/lib/.build-id/49/7291118bdb8c9dcf5055b5c43038d5079a20eb
/usr/lib/.build-id/4e
/usr/lib/.build-id/4e/c281704c4e4ffec76e8262b44bfff15a546b8b
/usr/lib/.build-id/50
/usr/lib/.build-id/50/dae78dd3148a6eb61ea0be15b78a334ebfc0a4
/usr/lib/.build-id/61
/usr/lib/.build-id/61/9389ad21d92879a36ce55eef102933441c99c3
/usr/lib/.build-id/91
/usr/lib/.build-id/91/e673517a09be108acf19a474786a4050abbe16
/usr/lib/.build-id/af
/usr/lib/.build-id/af/30c9b3791348c38f16bc9afa39091a4ebf72d4
/usr/lib/.build-id/cc
/usr/lib/.build-id/cc/ecce67bd627cc7b134250c1f74e5143aa6bf02
/usr/lib/.build-id/d5
/usr/lib/.build-id/d5/9f664f5744526edde7c3a7af400da1ecf29643
/usr/lib/.build-id/d6
/usr/lib/.build-id/d6/4debb4af826abe7deb67ce72754aa177063963
/usr/lib/.build-id/e8
/usr/lib/.build-id/e8/cb0e6da586a9d0494ebcd9fbf75d1ab70c3daa
/usr/lib/.build-id/ef
/usr/lib/.build-id/ef/03f72e3990b5501c2f3f16f5fc38147ff6eefa
/usr/share/doc/fastx_toolkit
/usr/share/doc/fastx_toolkit/AUTHORS
/usr/share/doc/fastx_toolkit/COPYING
/usr/share/doc/fastx_toolkit/NEWS
/usr/share/doc/fastx_toolkit/README
/usr/share/doc/fastx_toolkit/THANKS
References
Summary
In this tutorial we learn how to install fastx_toolkit on Fedora 36 using yum and [dnf]((/fedora/36/dnf/).
