Introduction
In this tutorial we learn how to install bowtie2 on CentOS 8.
What is bowtie2
Bowtie 2 is an ultra fast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
We can use yum or dnf to install bowtie2 on CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install bowtie2.
Install bowtie2 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 bowtie2 using dnf by running the following command:
sudo dnf -y install bowtie2
Install bowtie2 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 bowtie2 using yum by running the following command:
sudo yum -y install bowtie2
How To Uninstall bowtie2 on CentOS 8
To uninstall only the bowtie2 package we can use the following command:
sudo dnf remove bowtie2
bowtie2 Package Contents on CentOS 8
/usr/bin/bowtie2
/usr/bin/bowtie2-align-l
/usr/bin/bowtie2-align-s
/usr/bin/bowtie2-build
/usr/bin/bowtie2-build-l
/usr/bin/bowtie2-build-s
/usr/bin/bowtie2-inspect
/usr/bin/bowtie2-inspect-l
/usr/bin/bowtie2-inspect-s
/usr/lib/.build-id
/usr/lib/.build-id/18
/usr/lib/.build-id/18/bad035629a4ca1daf523aa269fd3d958e09aa0
/usr/lib/.build-id/79
/usr/lib/.build-id/79/98d757ca706b4da4a1f060536c3eed2caeb5e8
/usr/lib/.build-id/91
/usr/lib/.build-id/91/6fae9a8def67662263cd7316804a1135ed297b
/usr/lib/.build-id/9a
/usr/lib/.build-id/9a/cefd8e81b5568a79b338cd647311284ce05f56
/usr/lib/.build-id/b0
/usr/lib/.build-id/b0/0d6d174c4107f7fe2faf4bfa542745ac698c1f
/usr/lib/.build-id/d8
/usr/lib/.build-id/d8/686fd7823e43a5c4f0692f8a6e8a74a4e7a04f
/usr/share/doc/bowtie2
/usr/share/doc/bowtie2/AUTHORS
/usr/share/doc/bowtie2/MANUAL
/usr/share/doc/bowtie2/MANUAL.markdown
/usr/share/doc/bowtie2/NEWS
/usr/share/doc/bowtie2/TUTORIAL
/usr/share/licenses/bowtie2
/usr/share/licenses/bowtie2/LICENSE
/usr/share/man/man1/bowtie2-build.1.gz
/usr/share/man/man1/bowtie2-inspect.1.gz
/usr/share/man/man1/bowtie2.1.gz
References
Summary
In this tutorial we learn how to install bowtie2 on CentOS 8 using yum and dnf.
