About the differences of index-building process between Bowtie and BWA

Question

[ghostforever.shi]

Hi, everyone, I have a problem about the difference between Bowtie and BWA. It is said that BWA first built the suffix array and then generate the BWT. Bowtie use BWT to compress the FM-index. I wonder what's the difference between these two process? Thanks.

[h.mon]

I guess the best source of information for your question are the source codes, but not many people are proficient at the level required. It would be a very good exercise, in case you want to further your programming skills. By the way, bwa and bowtie or bowtie2 are far better tags than next-gen and alignment.

[ghostforever.shi]

Oh, I got it, thanks a lot.