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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Alternate assembly seqences in Primary assembly seqence position #51

Open Xuelei-Dai opened 3 years ago

Xuelei-Dai commented 3 years ago

Hello, For the hifisam software to assembly the genome, we can get the *.a_ctg.gfa and *.p_utg.noseq.gfa file, but I want to know the
position of the *.a_ctg.gfa sequences in *.p_utg.noseq.gfa seqences, how to get it?

Best wishes

chhylp123 commented 3 years ago

You can grep the read names (A-lines) of *.a_ctg.gfa at *.p_utg.noseq.gfa. A-lines indicate the positions of read at unitigs. By the way, *.r_utg.noseq.gfa is lossless while *.p_utg.noseq.gfa pops small bubbles.