How To Install bowtie on CentOS 8

bowtie is An ultrafast, memory-efficient short read aligner

Introduction

In this tutorial we learn how to install bowtie on CentOS 8.

What is `bowtie`

Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10

We can use yum or dnf to install bowtie on CentOS 8. In this tutorial we discuss both methods but you only need to choose one of method to install bowtie.

Install bowtie 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 bowtie using dnf by running the following command:

sudo dnf -y install bowtie

Install bowtie 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 bowtie using yum by running the following command:

sudo yum -y install bowtie

How To Uninstall bowtie on CentOS 8

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

sudo dnf remove bowtie

bowtie Package Contents on CentOS 8

/usr/bin/bowtie
/usr/bin/bowtie-align-l
/usr/bin/bowtie-align-l-debug
/usr/bin/bowtie-align-s
/usr/bin/bowtie-align-s-debug
/usr/bin/bowtie-build
/usr/bin/bowtie-build-l
/usr/bin/bowtie-build-l-debug
/usr/bin/bowtie-build-s
/usr/bin/bowtie-build-s-debug
/usr/bin/bowtie-inspect
/usr/bin/bowtie-inspect-l
/usr/bin/bowtie-inspect-l-debug
/usr/bin/bowtie-inspect-s
/usr/bin/bowtie-inspect-s-debug
/usr/lib/.build-id
/usr/lib/.build-id/00
/usr/lib/.build-id/00/31f9fc30b4b44f84708d02da21f90430c6f1b8
/usr/lib/.build-id/0d
/usr/lib/.build-id/0d/e35faf8ee6b766edf6c3277525d92ffdf02feb
/usr/lib/.build-id/25
/usr/lib/.build-id/25/8072302f5f6386982ef1153942aaad375e02ed
/usr/lib/.build-id/4c
/usr/lib/.build-id/4c/96e7db48d05480a0bf66a70c83ec4a4da9384d
/usr/lib/.build-id/57
/usr/lib/.build-id/57/05b921fefb38e3596086f72493cdd185c44d6f
/usr/lib/.build-id/69
/usr/lib/.build-id/69/b9b39fa724ace66bb9b8cd091f1f453340c359
/usr/lib/.build-id/81
/usr/lib/.build-id/81/a68497086c8c9f50a7f2bfd65d6b31d6f2850e
/usr/lib/.build-id/82
/usr/lib/.build-id/82/7b7d97a43ee77d37508b1749853eb1986d6953
/usr/lib/.build-id/aa
/usr/lib/.build-id/aa/654f3cac011a6f74677434a740e933a333a63c
/usr/lib/.build-id/b0
/usr/lib/.build-id/b0/77db3f90088cedbf577eef9ea0c1795369dbcb
/usr/lib/.build-id/cc
/usr/lib/.build-id/cc/c401b17213a0ee796162a58c3039b8674277c8
/usr/lib/.build-id/df
/usr/lib/.build-id/df/980c30578ec3c5a881a102f59ea51c3ee296f0
/usr/share/bowtie
/usr/share/bowtie/genomes
/usr/share/bowtie/genomes/NC_008253.fna
/usr/share/bowtie/indexes
/usr/share/bowtie/indexes/e_coli.1.ebwt
/usr/share/bowtie/indexes/e_coli.2.ebwt
/usr/share/bowtie/indexes/e_coli.3.ebwt
/usr/share/bowtie/indexes/e_coli.4.ebwt
/usr/share/bowtie/indexes/e_coli.README
/usr/share/bowtie/indexes/e_coli.rev.1.ebwt
/usr/share/bowtie/indexes/e_coli.rev.2.ebwt
/usr/share/bowtie/reads
/usr/share/bowtie/reads/e_coli_1000.fa
/usr/share/bowtie/reads/e_coli_1000.fq
/usr/share/bowtie/reads/e_coli_1000.raw
/usr/share/bowtie/reads/e_coli_10000snp.fa
/usr/share/bowtie/reads/e_coli_10000snp.fq
/usr/share/bowtie/reads/e_coli_1000_1.fa
/usr/share/bowtie/reads/e_coli_1000_1.fq
/usr/share/bowtie/reads/e_coli_1000_2.fa
/usr/share/bowtie/reads/e_coli_1000_2.fq
/usr/share/bowtie/reads/e_coli_1000_interleaved.fq
/usr/share/bowtie/scripts
/usr/share/bowtie/scripts/best_verify.pl
/usr/share/bowtie/scripts/bowtie-hbb.sh
/usr/share/bowtie/scripts/bs_mapability.pl
/usr/share/bowtie/scripts/build_test.sh
/usr/share/bowtie/scripts/colorize_fasta.pl
/usr/share/bowtie/scripts/colorize_fastq.pl
/usr/share/bowtie/scripts/convert_quals.pl
/usr/share/bowtie/scripts/fastq_to_tabbed.pl
/usr/share/bowtie/scripts/gen_2b_occ_lookup.pl
/usr/share/bowtie/scripts/gen_dnamasks2colormask.pl
/usr/share/bowtie/scripts/gen_occ_lookup.pl
/usr/share/bowtie/scripts/gen_solqual_lookup.pl
/usr/share/bowtie/scripts/infer_fraglen.pl
/usr/share/bowtie/scripts/make_a_thaliana_tair.sh
/usr/share/bowtie/scripts/make_b_taurus_UMD3.sh
/usr/share/bowtie/scripts/make_c_elegans.sh
/usr/share/bowtie/scripts/make_canFam2.sh
/usr/share/bowtie/scripts/make_d_melanogaster.sh
/usr/share/bowtie/scripts/make_e_coli.sh
/usr/share/bowtie/scripts/make_galGal3.sh
/usr/share/bowtie/scripts/make_h_sapiens_ncbi36.sh
/usr/share/bowtie/scripts/make_h_sapiens_ncbi37.sh
/usr/share/bowtie/scripts/make_hg18.sh
/usr/share/bowtie/scripts/make_hg19.sh
/usr/share/bowtie/scripts/make_m_musculus_ncbi37.sh
/usr/share/bowtie/scripts/make_mm8.sh
/usr/share/bowtie/scripts/make_mm9.sh
/usr/share/bowtie/scripts/make_rn4.sh
/usr/share/bowtie/scripts/make_s_cerevisiae.sh
/usr/share/bowtie/scripts/mapability.pl
/usr/share/bowtie/scripts/pe_verify.pl
/usr/share/bowtie/scripts/reconcile_alignments.pl
/usr/share/bowtie/scripts/reconcile_alignments_pe.pl
/usr/share/bowtie/scripts/run-hbb.sh
/usr/share/doc/bowtie
/usr/share/doc/bowtie/AUTHORS
/usr/share/doc/bowtie/MANUAL
/usr/share/doc/bowtie/NEWS
/usr/share/doc/bowtie/TUTORIAL
/usr/share/doc/bowtie/VERSION
/usr/share/doc/bowtie/manual.html
/usr/share/doc/bowtie/style.css
/usr/share/licenses/bowtie
/usr/share/licenses/bowtie/GPL.txt
/usr/share/licenses/bowtie/LGPL.txt
/usr/share/licenses/bowtie/LICENSE

References

bowtie website

Summary

In this tutorial we learn how to install bowtie on CentOS 8 using yum and dnf.