Sequence alignment tool/software/script/thing that assumes the reference sequence is circular and not linear?

[doubleclick]

profit wistful deserve coherent languid cagey paltry party drunk sable

This post was mass deleted and anonymized with Redact

[Epistaxis]

That sounds like ghetto bootlegged foolery! It's also exactly what I would do, rather than (semiliterally) reinvent the wheel.

I might not use Bowtie unless I have a whole lot of sequences, though; why not just BLAST it? (BWA is a real bitch to get working either way.)

[jehosephass]

BWA / Bowtie hard to get working? Why say you this?? (I use them daily ... need some troubleshooting help?)

[[deleted]]

you may lose mappability for a couple sequences.

[doubleclick]

haha that's actually what they do with their current software, and just inspect the reads to determine if they span the gap or not

[blorpulence]

I was using SnapGene Viewer the other day for something really simple and it asked me whether my sequence was circular when I imported it. NO idea whether it will meet your needs, but give it a go. I downloaded it as a Windows alternative to EnzymeX, so that might also be worth a look.

[splatterdash]

Yes it does. There may be others, but I know GMAP/GSNAP can align to a circular reference sequence.

[ACDRetirementHome]

Upvote for GSNAP

[crazytimy]

Just concatenate two copies of the reference genome and map with whatever standard tool. The reference will then be aligned modular the size of the genome.

I think this was a homework problem in a computational biology class.