Deciding on the best read length for metagenomics

Question

[capfz200]

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?

Answer 1

[colindaven]

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.