bfast
- Indy Siva
Introduction
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.
Usage
module load bioinformatics/bfast/0.7.0a
module display bioinformatics/bfast/0.7.0a ------------------------------------------------------------------- /sw/com/modulefiles/bioinformatics/bfast/0.7.0a: module-whatis adds BFAST directories to PATH etc. prepend-path PATH /sw/bioinformatics/bfast/0.7.0a/bin -------------------------------------------------------------------
Installation
yum install bzip2-devel mkdir -p /sw/bioinformatics/bfast/0.7.0a/SRC cd /sw/bioinformatics/bfast/0.7.0a/SRC tar -zxvf bfast-0.7.0a.tar.gz cd /sw/bioinformatics/bfast/0.7.0a/SRC/bfast-0.7.0a ./configure --prefix=/sw/bioinformatics/bfast/0.7.0a make make check make install