How To Install fastx_toolkit on Fedora 34

fastx_toolkit is Tools to process short-reads FASTA/FASTQ files

Introduction

In this tutorial we learn how to install fastx_toolkit on Fedora 34.

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 34. 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 34 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

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 34 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

The output should look something like this:

Fedora 34 - x86_64                               20 kB/s | 6.6 kB     00:00
Fedora 34 openh264 (From Cisco) - x86_64        1.4 kB/s | 989  B     00:00
Fedora Modular 34 - x86_64                       68 kB/s | 6.5 kB     00:00
Fedora 34 - x86_64 - Updates                    3.5 kB/s | 6.2 kB     00:01
Fedora Modular 34 - x86_64 - Updates             17 kB/s | 5.9 kB     00:00
Metadata cache created.

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 34

To uninstall only the fastx_toolkit package we can use the following command:

sudo dnf remove fastx_toolkit

fastx_toolkit Package Contents on Fedora 34

/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/08
/usr/lib/.build-id/08/9fc8e707e37c2c75bc69f2b68d03f5bba9838c
/usr/lib/.build-id/0d
/usr/lib/.build-id/0d/758a4d1193dcbc366c6daaf2274ea6aa5c3c96
/usr/lib/.build-id/3a
/usr/lib/.build-id/3a/ab1cf95f0c40c0fa05d632ffeb6c1679c0a601
/usr/lib/.build-id/3e
/usr/lib/.build-id/3e/825f7dff03d349bedf6e36db23bb420f0773cd
/usr/lib/.build-id/45
/usr/lib/.build-id/45/ffd4f205a129407dc29f9cc0ce360d41d58718
/usr/lib/.build-id/47
/usr/lib/.build-id/47/eabe7545902837c5077e250fa8b7df78f9d7b8
/usr/lib/.build-id/50
/usr/lib/.build-id/50/15158c6babd7f35d83c6a24f098dfc23f9a4a1
/usr/lib/.build-id/54
/usr/lib/.build-id/54/2da25c3e2c587d795a5634a4490040b09ca72f
/usr/lib/.build-id/5d
/usr/lib/.build-id/5d/e9584bf4dbb0d21b235fe58e75771c082506dc
/usr/lib/.build-id/9a
/usr/lib/.build-id/9a/8c88bbedf67f071af74b10ba302a358776dd31
/usr/lib/.build-id/bd
/usr/lib/.build-id/bd/43f8d28c4ed1c06aa1b759821f8250720774c2
/usr/lib/.build-id/bf
/usr/lib/.build-id/bf/b79f6bfad2301a77676234c336d2d4a4284a8c
/usr/lib/.build-id/d2
/usr/lib/.build-id/d2/8cea6cac8737df79654074915e6bbda28fa110
/usr/lib/.build-id/d7
/usr/lib/.build-id/d7/1867fe4176a8c19445c7d038dc661a11f6b8eb
/usr/lib/.build-id/f7
/usr/lib/.build-id/f7/67c3ea6e1ac85b64d98986ea49c6772a0454eb
/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

fastx_toolkit website

Summary

In this tutorial we learn how to install fastx_toolkit on Fedora 34 using yum and dnf.