minimap2 icon indicating copy to clipboard operation
minimap2 copied to clipboard

GFA file output size

Open GeorgeBGM opened this issue 1 year ago • 0 comments

Hi, I want to align the assembled sequence (HJ.stLFR_CCS.maternal.fasta.gz HJ.stLFR_CCS.paternal.fasta.gz) to the human HPRC reference sequence (HPRC.Phase1.CHM13v2_Non-W.gfa) using the following command. The final GFA output (out.gfa) is smaller than the HPRC file, so how do we keep the entire HPRC reference sequence and add the assembled sequence to it as well.

 _minigraph  -cxggs  --ggen -l10k   HPRC.Phase1.CHM13v2_Non-W.gfa   HJ.stLFR_CCS.maternal.fasta.gz HJ.stLFR_CCS.paternal.fasta.gz  -t 30 > out.gfa_
 
 I'm looking forward to your reply

GeorgeBGM avatar Jun 09 '23 06:06 GeorgeBGM