which alignment tool is better to use to align genome on short reference sequence ~5000b.p

Question

[bbb]

I have 22 reference sequences with length about 5000 b.p. Which alignment tool is better to use to align genome on short reference sequence?

Is bwa-MEM the preferred algorithm?

I used 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

[h.mon]

align genome on short reference sequence

I don't understand what are you aligning:

• align a genome to another (reference) small genome;

• or align some sequencing reads to a short reference genome.

In the first case, BLAT / BLAST / NUCmer are good, in the second, BWA-mem and Bowtie2 will work fine. Bowtie2 in particular is a short read mapper, so it will only work properly in the second case, but BWA-mem may be used in the firstcase as well.

The comment refers to the fact BLAT / BLAST / NUCmer will be more sensitive than Bowtie2 and BWA, but unless you are mapping some distantly related sequences, the difference will be small

[Sej Modha]

I would use BLAT or NUCMER in such cases.