Couldn'T Understand Re-Seeding Option In Bowtie2

Question

[ancient_learner]

I was just wondering what the re-seeding option actually mean in bowtie2 manual. I have gone through it but couldnt understand actual logic in setting it.

Answer 1

[Ido Tamir]

ATTENTION: bowtie2 and multiple hits. Some people found it strange, that a read with identical name,qualities and sequence will always map to the same position although equally good positions exist. However when I align something and then somebody does the analysis again we indeed would like to get the identical output, which is the default behaviour.

--non-deterministic breaks this and randomizes the positions for reads with identical name, qualities and sequence by adding the time for the seed of the PRG. The case of having reads with identical names is rather artificial (or you might have it with sequences in raw format).