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
- how to use this information in extending the contigs and scaffolding?
- which reads of Illumina are not mapped to the contigs?
- how to sort those illumina reads based on the depth/coverage on each contigs?
- Are there any software/tool for this purpose?
Any suggestions or comments?
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