How To Install bfast on Fedora 36

In this tutorial we learn how to install bfast in Fedora 36. bfast is Blat-like Fast Accurate Search Tool

Introduction

In this tutorial we learn how to install bfast on Fedora 36.

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 36. In this tutorial we discuss both methods but you only need to choose one of method to install bfast.

Install bfast on Fedora 36 Using dnf

Update yum database with dnf using the following command.

sudo dnf makecache --refresh

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

sudo dnf -y install bfast

Install bfast on Fedora 36 Using yum

Update yum database with yum using the following command.

sudo yum makecache --refresh

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 36

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

sudo dnf remove bfast

bfast Package Contents on Fedora 36

/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/14
/usr/lib/.build-id/14/07965947c6eafa282c8cb907fa1416b1610893
/usr/lib/.build-id/2d
/usr/lib/.build-id/2d/c23cca5612ccf9f5a935fa29b02ad38b6006f3
/usr/lib/.build-id/32
/usr/lib/.build-id/32/74c36186a65774317f880c4d50385fbe782c43
/usr/lib/.build-id/76
/usr/lib/.build-id/76/3c9c608acef851668c2e05eeaca58e2de12902
/usr/lib/.build-id/9e
/usr/lib/.build-id/9e/e455cdb6f98617927e7281a301a068f91c573d
/usr/lib/.build-id/c2
/usr/lib/.build-id/c2/386b69bca2103874557d01f43f1523cd99f46a
/usr/lib/.build-id/c4
/usr/lib/.build-id/c4/d64ff5698b4f0a7e8c9e68ce78f1c51a980bb0
/usr/lib/.build-id/ca
/usr/lib/.build-id/ca/99b754c87e11af65e27f50c446a8a0acbed13b
/usr/lib/.build-id/cb
/usr/lib/.build-id/cb/f63028a1161e46b6d422716b65f9a959e57c67
/usr/lib/.build-id/da
/usr/lib/.build-id/da/6944447c7563977f825a31483e78a7561cf8e7
/usr/lib/.build-id/e4
/usr/lib/.build-id/e4/9239a9f26302b0a59c82088f3a9be1dd1cfdf5
/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

bfast website

Summary

In this tutorial we learn how to install bfast on Fedora 36 using yum and [dnf]((/fedora/36/dnf/).