How To Install bowtie on Rocky Linux 8

In this tutorial we learn how to install bowtie on Rocky Linux 8. bowtie is An ultrafast, memory-efficient short read aligner

Introduction

In this tutorial we learn how to install bowtie on Rocky Linux 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 Rocky Linux 8. In this tutorial we discuss both methods but you only need to choose one of method to install bowtie.

Install bowtie on Rocky Linux 8 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

After updating yum database, We can install bowtie using dnf by running the following command:

sudo dnf -y install bowtie

Install bowtie on Rocky Linux 8 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

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 Rocky Linux 8

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

sudo dnf remove bowtie

bowtie Package Contents on Rocky Linux 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 Rocky Linux 8 using yum and dnf.