aligning reads varying from 110bp to 56520bp to a reference sequence

Question

[cecilio11]

Hi Biostars,

I have a set of sequences (from a genome sequencing file) that mapped to a reference sequence (let's name it "ref1"). The file containing the mapped sequences could be named "mapped_ref1". The sizes of those sequences vary from 110bp to 56520bp. Those sequences do not represent the whole genome, but several genes. I want to identify a set of those genes by sequencing them.

I want to sequence genes that have: 1) the highest identity to the reference genome 2) highest coverage.

I am planning on aligning the sequences on "mapped_ref1" to the reference sequence "ref1". After I obtain the alignments, I can blast the genes to identify them and to find the ones with the highest identity to the "ref1" genes. Then I will choose the ones with the highest coverage.

Dear biostars, what tools would you recommend to do this job?

Would you recommend a different strategy to accomplish the job at hand?

Best regards,

cecilio11

[Joe]

Tool requests are Question posts, not Tool posts (the latter are for announcements of new software etc). I’ve changed it for you this time, but please bear it in mind for the future.

[lieven.sterck]

Can you elaborate on the "highest coverage" part of your question?

You seem to already have sequences to work with, so why do you then want to sequence them again?