Information about the package, bfast, which is shipped with common Linux distributions. The bfast package is designed for, Blat-like Fast Accurate Search Tool.
Package Name:
bfast
Summary:
Blat-like Fast Accurate Search Tool
Description:
BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: Speed: enables billions of short reads to be mapped quickly. Accuracy: A priori probabilities for mapping reads with defined set of variants. 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.
Architecture:
x86_64
Version:
0.7.0a
Release:
1.el6
Size:
685 k
Repository:
epel
From Repository:
Licence:
GPLv2 and MIT
Control the bfast package with the following handy commands outlined below.
yum install bfast
This command will install bfast on the server.
yum remove bfast
This command will un-install bfast on the server. When you run this command, you will be asked if you are sure that you want to remove bfast, so you have to manually confirm that you want to do this.
yum -y remove bfast
This command will un-install bfast on the server. When you run this command with th e -y flag, you will not be prompted to check that you are sure you want to remove the package - so be sure you absolutely want to remove bfast when using the -y flag.
yum update bfast
This command will update bfast to the latest version. When you run this command, you will be asked if you are sure that you want to remove bfast, so you have to manually confirm that you want to do this.
yum -y update bfast
This command will update bfast to the latest version. When you run this command with the -y flag, you will not be prompted to check that you are sure you want to remove the package - so be sure you absolutely want to remove bfast when using the -y flag.
yum info bfast
This command will show you core information about the bfast package.
yum deplist bfast
This command will show you the dependencies for bfast. Thankfully, when using Yum, if dependencies are required, these are also installed at the same time so you don't have to worry too much about that.
yum check-update bfast
This command will check if there is an update waiting on bfast. When you run this command this will return nothing if there is nothing to update, or, will return the package name if the package is due to be updated.