BWA aln vs. mem for 100bp reads

Question

[ropolocan]

Hello everyone,

Which BWA algorithm is a better choice for aligning 100 bp Illumina reads? BWA aln or BWA mem? I have read that BWA mem is usually faster, and more accurate, but what is BWA aln useful for then? Thanks.

Answer 1

[GenoMax]

When and why is bwa aln better then bwa mem?
and BWA-MEM Vs BWA-ALN (check blog link in @Goutham's comment)

[ropolocan]

Thank you so much, @genomax!