I faced a issue using bwa for some very shorts reads I have (49bp). I have numerous paired Illumina reads that I want to align against an assembly I made.
I saw this previous post about paired-reads aligning with several files : BWA mem on multiple samples , which propose to use bwa mem in a parallel way.
In bwa readme, it is written that, for reads shorter than 70bp, we should proceed this way :
bwa aln ref.fa read1.fq > read1.sai; bwa aln ref.fa read2.fq > read2.sai bwa sampe ref.fa read1.sai read2.sai read1.fq read2.fq > aln-pe.sam
When I tried this, the bwa aln part worked fine, but the bwa sampe step never ended. Considering that each file contain approximatively 8-10 Giga of data, I have no idea why it take so long (after 2days, I stopped the process).
What do you think about this ? Should I use an other aligner ?
Thanks for your advices,