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BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
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Pre-assembly binning? #271

Closed franciscozorrilla closed 3 years ago

franciscozorrilla commented 4 years ago

Hello again!

I have been thinking about how to increase the number and improve the quality of reconstructed MAGs, and I wanted to get your thoughts on a particular approach that I read in some bioinformatics paper (which I am now unable to find!).

Do you foresee any limitations or problems with performing an additional round of binning before assembly? The idea would be to bin short reads into pre-MAG bins (in order to reduce the complexity of assembly) and then assemble each of those pre-MAG bins. I imagine that these assemblies would probably include a number of closely related species or strains. Then I would perform a second round of binning using each of the generated assemblies, which would perhaps yield a greater number/more complete MAGs? Have you successfully used this double binning approach with CONCOCT before? If so please let me know how it went!

Best wishes, Francisco

franciscozorrilla commented 3 years ago

For example: https://www.biorxiv.org/content/10.1101/2020.04.03.021501v2

andand commented 3 years ago

Dear Francisco, I have not tried that, but a general problem with assembly and binning is the presence of closely related strains in the same assembly. The reads from these cause a lot of bubbles to form in the assembly graph, resulting in short contigs. I don't think the approach that you propose will solve that problem, but I may be wrong. Cheers Anders

On Wed, May 12, 2021 at 2:59 PM Francisco Zorrilla @.***> wrote:

For example: https://www.biorxiv.org/content/10.1101/2020.04.03.021501v2

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franciscozorrilla commented 3 years ago

Dear Anders, Thank you for your response. Indeed metagenomic assembly can be quite tricky for some metagenomes. I did some further reading and it appears that assemble-first and bin-first strategies can recover complementary and distinct genomes. Best wishes, Francisco