How to extend assembled PACBIO contigs for scaffolding



I have assembled a genome (PacBio HiFi) into contigs using IPA and Hifiasm. Those contigs were aligned to the Illumina mate pair reads of different sizes 2,5,7,10 kb using BWA-MEM so as to extend it for scaffolding. This generated .sam file. I tried SAMTOOLS after BWA-MEM alignment and received .bam, coverage, stat and depth file.

I am able to plot the depth of the individual contig/s and tried IGV tools. However, I am not sure about

  1. how to use this information in extending the contigs and scaffolding?
  2. which reads of Illumina are not mapped to the contigs?
  3. how to sort those illumina reads based on the depth/coverage on each contigs?
  4. Are there any software/tool for this purpose?

Any suggestions or comments?

Thank you




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