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xfengnefx / hifiasm-meta

hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
MIT License
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contig coverage #28

Open Sung-hub opened 1 year ago

Sung-hub commented 1 year ago

I ran hifiasm-meta HiFi reads from rumen microbiome and the contigs were generated from various bacterial and eukaryotes. I am wondering if I can find out the coverage of each contigs. Is there any hifiasm-meta output file can provide coverage information of each contigs? or is there any way to extract the coverage information?

xfengnefx commented 1 year ago

You can use the dp:f tag in S lines of hifiasm-meta's contig graph GFA files. The coverage is calculated by collecting all reads belonging to a contig in question. This considers contained reads.

If the contig is short and has only a couple of reads, this estimation is unreliable. For long contigs of hundreds of kilobases or >1Mb, it is largely in agree with read alignment-based estimations (e.g. jgi_summarize_bam_contig_depths of metabat2) in my experience.