Can i use bwa aln to align my illumina sequence whose length is 150 bp?

Question

[Zeason]

just like the topic. I got 150bp length illumina sequence data , can i use bwa aln to align it? Maybe should i use bwa mem to do this work?

Answer 1

[Arup Ghosh]

According to BWA documentation, you can go up to 1Mbp with BWA MEM.

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.