is it possible to use fasta files from different assembly softwares to create a circular fasta

jfass / apc

(a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join

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is it possible to use fasta files from different assembly softwares to create a circular fasta #3

Closed LuffyLuffy closed 5 years ago

LuffyLuffy commented 5 years ago

Hi, apc.pl is fast to tell whether a single sequence is a circular chromosome or plasmid.
I wonder if it possible to use different assembly result to realize a circular fasta file, that is, gap closer by different assembly results. Presently, we use paired blast and based on the blast result, to extend the fasta file, and finally got a circular chromosome.

jfass commented 5 years ago

I think there are better tools to do that kind of thing, like the PB-Suite ... or Circlator? ... though I don't have any direct experience with the latter. I hope that helps.

I don't have immediate plans to improve apc, but I'll keep your suggestion in mind if I do! ~Joe