How can I map 10k sequences to 1k genomes at a faster speed? Is there any tool

Question

[xeeoff]

I am trying to map more than 10k sequences to over 1000 genomes. Is they any tool I can do the mapping in a fast way?

[GenoMax]

It would be helpful to have information about range of sizes of both query and genome sequences. Depending on that information recommendations can be significantly different. There are plenty of tools available and as long as you have access to right hardware should be doable.

[Joe]

I think minimap2 is probably one of the fastest from what I've been hearing.

What are you trying to do? Do you care about coverage? You could downsample your reads to reduce the computation time if necessary.

[WouterDeCoster]

You probably should elaborate on what the application is here.

Answer 1

[gb]

With bowtie2 or BWA, there are more options. You are not giving enough information. How are you doing it now?