Combining contigs from separate assemblies

[Zoey Werbin]

Hi Anvi'o community,

I have about 50 metagenomes that were assembled separately into contigs. I'd like to carry out a similar binning workflow to the one described in this post, except without the co-assembly. To do this, it seems I need to concatenate the FASTA files with each sample's contigs (into a single contigs database), then map each sample to the concatenated contigs database. Then, I'll use the workflow described in the blog post (merging each sample's profile, then clustering contigs). 

However, this 2016 thread mentions that when combining contig files, "multiple scaffolds might overlap (i.e., same part of a genome). It would dilute mapping signal and render the analysis noisy and difficult." Does the anvi-cluster-contigs function essentially fix this problem? Or could something like anvi-dereplicate-genomes be used to remove almost-duplicate contigs? 

Thank you for any pointers! 

Zoey

[A. Murat Eren]

Hi Zoey,

I think the best practice would be to reconstruct genomes from your individual samples, then pool all genomes together and de-replicate them to generate a final non-redundant genomic collection, then use that collection to recruit reads from all samples to study their distribution across samples and population structures.

Best wishes,

--

A. Murat Eren (Meren) | he/him
http://merenlab.org :: twitter

--
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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