22 reference sequences with length about
Which alignment tool is better to use to align genome on short reference sequence?
bwa-MEM the preferred algorithm?
bowtie2, however it doesn't supposed to work good enough with short reference sequence.
From bowtie2 manual:
If your goal is very sensitive alignment to a relatively short reference sequence (e.g. a bacterial genome), this can be done with Bowtie 2 but you may want to consider using tools like NUCmer, BLAT, or BLAST. These tools can be extremely slow when the reference genome is long, but are often adequate when the reference is short