BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.
module load bwa bwa
For each of the BWA algorithms, you must first index the genome with the following command:
bwa index [options] input.fasta
#PBS -l nodes=2:ppn=8,pmem=1000mb,walltime=8:00:00 #PBS -m abe #PBS -M email@example.com module load bwa bwa index input.fasta bwa aln -t $PBS_NP input.fasta input.fq > output.sai
bwa aln bwa samse bwa sampe
A complete list of options for each of the algorithms is available at the BWA manual page.