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Deciding on the best read length for metagenomics

Greetings,

Currently, I am performing a study on microbial diversity on low diversity environments, and I have some questions about the best platform to use. I am planning to use NovaSeq 6000 to sequence my metagenomic DNA, and I have two options: Paired End 150 and Paired End 250. I would like to know how much do I gain in metagenome assembly and gene detection with long inserts versus short when compared to losing a bit of accuracy in the R2?

assembly sequencing next-gen
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updated by colindaven colindaven • written by capfz200 • capfz200

1 answer

It sounds like you want to do assembly after sequencing. In that case, always, always, always go for the longest read lengths you possibly can. It's not really a surprise than ONT and Pacbio HiFi and completely dominating the assembly realm, in metagenomics as well.

  • SE and PE 75bp are not great, except for alignment based metagenomics
  • You will definitely get better assemblies with 2x250bp.

How much better ? That's a tricky one, and dependent on your samples and their genomes, and how many close relatives they have. Perhaps you can go 2x250bp for a first run, subsample to 2x150bp and see if your assemblies are still useful.

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written by colindaven colindaven

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