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lh3 / miniwfa

A reimplementation of the WaveFront Alignment algorithm at low memory
MIT License
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miniwfa on syntenic regions #2

Closed diego-rt closed 2 years ago

diego-rt commented 2 years ago

Hi,

I would like to use miniwfa heuristic mode to align a 3 Mbp region from the Axolotl genome to its 200 kbp syntenic region in the human genome, with a particular emphasis on aligning any common repetitive regions as best as possible.

I was wondering whether you could give me your feedback as to whether this is the most suitable WFA implementation to achieve this with reasonable time and memory requirements? I have several thousands of such sequence pairs, which makes these requirements problematic.

In addition, am I correct in assuming that the test-mwf -c output is in paf format? Any advice on how to convert this format to fasta .aln or sam formats for further processing of the alignment?

Thanks in advance!

lh3 commented 2 years ago

miniwfa may not be the best choice for your application. You may consider traditional genome alignment tools like LASTZ etc. I guess they will work better.