How to process Omni-C data for genome assembly
I have ten samples that were processed with Omni‑C sequencing, which I plan to use for phasing and scaffolding in a de novo genome assembly using Verkko. Based on my understanding, I expected to receive 20 FASTQ files in total (R1 and R2 for each sample). However, I was sent a much larger number of FASTQ files, and I’m unsure how to handle them. I’ve read the Omni‑C documentation Omni-C documentation, but the workflow is still not entirely clear to me. My main question is: should I merge all FASTQ files that correspond to the same sample name before proceeding, if so how do I do that or is there a recommended way to process these files as‑is?
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It depends on the tool. Verkko can take multiple Hi-C or Omni-C FASTQs per sample. Other tools allow only two FASTQs per sample; in that case, you’re fine to concatenate, combining files from the same sample and read direction.
Furthermore, I want to ask does Hifiasm take ONT Duplex data in place for HiFi data given that in terms of accuracy they are similar? I am hoping to follow this format:
hifiasm -o HG002.asm --dual-scaf --telo-m CCCTAA --h1 read1.fq.gz --h2 read2.fq.gz --ul ul.fq.gz HG002-HiFi.fq.gzwhere instead of usingHiFi.fq.gz, I useONT_Duplex.fq.gzFor Verkko, ONT duplex reads are supported: the current docs say that
--hifican take any combination of PacBio HiFi and/or ONT duplex reads.For hifiasm, ONT support exists, but through a separate
--ontoption (e.g., see here). I don’t have first-hand experience with this, and (as far I can tell [but I didn’t check carefully]) the docs refer only to simplex reads, so YMMV. (IMO, I wouldn’t assume interchangeability between HiFi and ONT duplex based on accuracy alone.)So, as a starting position, I would not treat ONT duplex as a drop-in replacement for HiFi in hifiasm. In that case, I would look through the repo docs/issues/etc. to see whether and how duplex reads are handled. If I didn’t find much or anything (including searches with a search engine and/or an LLM), I’d consider reaching out to the authors of hifiasm about this specific question.
Also, just for future reference, you may get better visibility/answers if you post this as a new question rather than as a nested comment, since it’s on a different subject from the original post (handling multiple Hi-C/Omni-C FASTQ files in Verkko).