Merging two assemblies from separate metagenomic runs

[Robert Danczak]

Hello Anvi'o Team,

Sorry for a potentially silly question, but I've run into an issue where I'm trying to analyze metagenomic samples from a time series that were run at separate times and were assembled separately, thus I have two separate contigs files and two mapping files. What is the best way to remedy this and permit merged anvi'o profiles in the event that the headers/deflines for both of the assemblies/mapping are the same (i.e. the first contig is named "scaffold_0" in sample 1 and sample 2)? Thanks for any help you can provide and thanks for the amazing program!

Bob

[Tom Delmont]

Hi Bob,

Happy to hear that you like anvi'o.

Would you consider doing a co-assembly of your metagenomic time series?

This way, you would have a single fasta file (and contigs.db) but multiple BAM files from the mapping of each sample. It is the workflow we routinely use and it works pretty well in most scenarios (except if your samples have almost nothing in common, which is unusual for a timeseries).

If you want to keep working on your single assemblies, then the only way to merge the scaffolds would be renaming headers first, and then concatenate. However, one issue is the fact that multiple scaffolds might overlap (i.e., same part of a genome). It would dilute mapping signal and render the analysis noisy and difficult. Another alternative would be to not merge fasta files but use all metagenomic samples for mapping to each fasta file. This way, you can recover genomes using differential coverage from each fasta file, and then maybe use a pangenomic workflow to identify redundant genomes in your collection.

Hope it helps,

Tom

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Robert Danczak]

Thanks for the help!

Co-assemblies actually sounds like a great idea which I was planning on exploring in the future, I was just wondering what alternatives could be utilized on a shorter notice which there appears to be a few. Thanks again for your help

Bob