Entering edit mode
2.6 years ago
zhousun21
▴
40
Hi all, Does anyone know a method to convert PAF to AGP?
The intent is to take the output of minimap2 and produce an AGP for genome finishing.
Other programs available (ex: RagTag and Racon) aren't really designed for this and don't handle overlaps very well.
Any advice will be appreciated.
try to put your true aim in the post. You are positing an XY problem where you say "if I can just convert PAF to AGP, then my problem is solved" but this might not be true. from what I can gather, you want to scaffold your draft genome assembly based on your alignment of a draft assembly to a reference genome. in this case, ragtag does seem like a good program to try. if you think overlaps are a problem, then ask a question specifically about that and what you have seen and what you have tried
Thanks, you're right.
Ragtag is a great program for what is was designed for.
I am trying to finish a genome by aligning contigs to a related species. Ragtag aligns target contigs to a reference (reference is chopped up first but I won't bore you with the details.) The issue is that if two contigs overlap on the reference, the correct action is to form an overlap on the resulting fasta. Ragtag isn't designed to do this, and they are clear on this point in the docs. Instead they either abut the overlapping contigs or insert a gap in between, and neither of these gives a good result for these purposes.
Instead I can generate a PAF (or SAM) output from minimap2, which has all the right information both for overlaps and gaps. But I'm stumped as to how to get from the minimap2 output to a properly assembled finished genome. I assume there is a way to convert PAF to AGP - all the data is there - but haven't been able to find anything.
I'd like to pat myself on the back for being incredibly resourceful, but really, I only googled convert PAF to AGP. Here is a top hit:
https://bioconvert.readthedocs.io/en/master/formats.html
What exactly did you search for?
Thanks for checking, but sadly that function is not supported with Bioconvert. Honorary pat on the back for you, though.