Introduction
In this tutorial we learn how to install bwa on CentOS 8.
What is bwa
BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
We can use yum or dnf to install bwa on CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install bwa.
Install bwa on CentOS 8 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install bwa using dnf by running the following command:
sudo dnf -y install bwa
Install bwa on CentOS 8 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
CentOS Linux 8 - AppStream 43 kB/s | 4.3 kB 00:00
CentOS Linux 8 - BaseOS 65 kB/s | 3.9 kB 00:00
CentOS Linux 8 - ContinuousRelease 43 kB/s | 3.0 kB 00:00
CentOS Linux 8 - Extras 23 kB/s | 1.5 kB 00:00
CentOS Linux 8 - FastTrack 40 kB/s | 3.0 kB 00:00
CentOS Linux 8 - HighAvailability 36 kB/s | 3.9 kB 00:00
CentOS Linux 8 - Plus 24 kB/s | 1.5 kB 00:00
CentOS Linux 8 - PowerTools 50 kB/s | 4.3 kB 00:00
Extra Packages for Enterprise Linux Modular 8 - x86_64 13 kB/s | 9.2 kB 00:00
Extra Packages for Enterprise Linux 8 - x86_64 24 kB/s | 8.5 kB 00:00
Metadata cache created.
After updating yum database, We can install bwa using yum by running the following command:
sudo yum -y install bwa
How To Uninstall bwa on CentOS 8
To uninstall only the bwa package we can use the following command:
sudo dnf remove bwa
bwa Package Contents on CentOS 8
/usr/bin/bwa
/usr/bin/qualfa2fq.pl
/usr/bin/xa2multi.pl
/usr/lib/.build-id
/usr/lib/.build-id/b4
/usr/lib/.build-id/b4/63fcc0428a04617c8c921ae9428f90e4505f08
/usr/share/bwa/bwakit
/usr/share/bwa/bwakit/README.md
/usr/share/bwa/bwakit/bwa-postalt.js
/usr/share/bwa/bwakit/run-HLA
/usr/share/bwa/bwakit/run-bwamem
/usr/share/bwa/bwakit/run-gen-ref
/usr/share/bwa/bwakit/typeHLA-selctg.js
/usr/share/bwa/bwakit/typeHLA.js
/usr/share/bwa/bwakit/typeHLA.sh
/usr/share/doc/bwa
/usr/share/doc/bwa/COPYING
/usr/share/doc/bwa/NEWS.md
/usr/share/doc/bwa/README-alt.md
/usr/share/doc/bwa/README.md
/usr/share/man/man1/bwa.1.gz
References
Summary
In this tutorial we learn how to install bwa on CentOS 8 using yum and dnf.
