Alternate assembly seqences in Primary assembly seqence position

[Xuelei-Dai]

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]

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.