Bwa Aln And Samse Options

Question

[Anjan]

BWA has two options aln and samse. From the online help manual and the BWA paper it seems that the aln option performs the alignment of the reads to reference. What function, then, does samse (and sampe) perform if the alignment is already done by the aln option? Thanks, Anjan

Answer 1

[Pierre Lindenbaum]

• aln aligns the reads and produces a file *.sai of all the possible candidates.
• samse works with the single ends, transforms the *.sai to *.sam "Repetitive hits will be randomly chosen. "
• sampe works with the paired ends, takes the pairs of alignments , transforms the two *.sai to one *.sam, and select the best hits according the orientations, distance between the reads, etc... " Repetitive read pairs will be placed randomly. "

[Anjan]

thank you Pierre