How To Install bfast on Fedora 34
Introduction
In this tutorial we learn how to install bfast on Fedora 34.
What is bfast
BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include Speed Accuracy An easy way to measurably tune accuracy at the expense of speed. Specifically, BFAST was designed to facilitate whole-genome resequencing, where mapping billions of short reads with variants is of utmost importance. BFAST supports both Illumina and ABI SOLiD data, as well as any other Next-Generation Sequencing Technology (454, Helicos), with particular emphasis on sensitivity towards errors, SNPs and especially indels. Other algorithms take short-cuts by ignoring errors, certain types of variants (indels), and even require further alignment, all to be the “fastest” (but still not complete). BFAST is able to be tuned to find variants regardless of the error-rate, polymorphism rate, or other factors.
We can use yum or dnf to install bfast on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install bfast.
Install bfast 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 bfast using dnf by running the following command:
sudo dnf -y install bfast
Install bfast 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 bfast using yum by running the following command:
sudo yum -y install bfast
How To Uninstall bfast on Fedora 34
To uninstall only the bfast package we can use the following command:
sudo dnf remove bfast
bfast Package Contents on Fedora 34
/usr/bin/balignmentscoredistribution
/usr/bin/balignsim
/usr/bin/bevalsim
/usr/bin/bfast
/usr/bin/bfast.resubmit.pl
/usr/bin/bfast.submit.pl
/usr/bin/bgeneratereads
/usr/bin/bindexdist
/usr/bin/bindexhist
/usr/bin/bmfmerge
/usr/bin/brepeat
/usr/bin/btestindexes
/usr/bin/ill2fastq.pl
/usr/bin/solid2fastq
/usr/lib/.build-id
/usr/lib/.build-id/3c
/usr/lib/.build-id/3c/f512555bfab26f7afbf2cf633e52157c8be74a
/usr/lib/.build-id/5d
/usr/lib/.build-id/5d/6383e8aed18ae395a305521a67d044d06d3d95
/usr/lib/.build-id/5f
/usr/lib/.build-id/5f/1545aae2ba17c4b9cb814be6044a8d22b94fab
/usr/lib/.build-id/79
/usr/lib/.build-id/79/8d746808e93b9663d3bc0fc149ffb54e2f763c
/usr/lib/.build-id/80
/usr/lib/.build-id/80/a8345c4e9c84a10fac6c15ed2531ce494e163c
/usr/lib/.build-id/89
/usr/lib/.build-id/89/e7bb1670ed78c5af535a2446b6fa44bcbe7745
/usr/lib/.build-id/b1
/usr/lib/.build-id/b1/f44ef8c3d4a73df7eda284ec370f0afc6e6d59
/usr/lib/.build-id/d1
/usr/lib/.build-id/d1/775acea80b645e12c247b58423cde0f342332d
/usr/lib/.build-id/e2
/usr/lib/.build-id/e2/15d14f8ac35b3341472ce5177f8c9e1bce67bc
/usr/lib/.build-id/ee
/usr/lib/.build-id/ee/748f937d1d1ee494c2b51235bb9100591d6b97
/usr/lib/.build-id/f4
/usr/lib/.build-id/f4/e727c3f2047dc4d43c97441e8109b2f51d4245
/usr/share/doc/bfast
/usr/share/doc/bfast/AUTHORS
/usr/share/doc/bfast/ChangeLog
/usr/share/doc/bfast/NEWS
/usr/share/doc/bfast/README
/usr/share/doc/bfast/bfast-book.pdf
/usr/share/licenses/bfast
/usr/share/licenses/bfast/LICENSE
References
Summary
In this tutorial we learn how to install bfast on Fedora 34 using yum and dnf.