5.3 years ago by
From the BWA site:
"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."
So it really depends on how long the reads are?
If greater than 100 bp try:
bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
if less than 100 bp try:
bwa aln ref.fa read1.fq > aln_sa1.sai
bwa aln ref.fa read2.fq > aln_sa2.sai
bwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam