20 Mate Alignment With Gaps To Reference Genome

Question

[sinverso]

I'm trying to align a string of twenty 5-mers with gaps of 100 to 400 bp to a reference genome. It's similar to paired-alignment except instead of N=2, N=20. The order of the twenty 5-mers is known.

Is there any software that can handle a data set like this?

Best regards,

-Sam

Answer 1

[Chris Miller]

Sounds similar to the reads produced by complete genomics (more info here: Has anyone had experience with Complete Genomics sequencing and data analysis?). I can't recall if they ever released their aligner for public consumption.

You might also look at some of the aligners that have been developed to work with PacBio's strobe sequencing mode, which produces similar (if longer) data.

[sinverso]

Yes, it's similar to Complete Genomics, unfortunately, they've not released their aligner and there's no aligner I've found that can work with their raw data. Thanks for the PacBio tip. Their 'short' reads are ~700 bp so it looks they just use BLAST, which won't quite work for my tiny 5 bp reads.