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Old 05-10-2016, 09:16 AM   #1
DL88
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Location: Pittsburgh

Join Date: May 2016
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Default Resolve species/strain in metagenomic bin

Hi all,

I am trying to recover microbial draft genomes from metagenomic contigs.

I have used several assembly and binning tools to optimize my results (CLC, Spades, Vizbin, Maxbin, Metabat).
Since my samples were dominated by one genus the majority of the contigs belong to this taxa, resulting in one big bin, which based on the number of extracted 16S sequences contains multiple species or even strains of this genus. None of the binning tools I have worked with have been able to resolve the bin, leaving me with one big "pan-genome" bin that is very complete, but also very contaminated (according to checkm).

What is the best way to resolve the bin? Are other binning softwares that are more accurate? I know of tools that offer metagenomic strain resolution, however usually a database with multiple already sequenced genomes is necessary for those, which in my case is not really the case.

Thank you for any insights on this topic.

Daniel
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Old 06-01-2016, 04:53 AM   #2
yzzhang
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Location: florida

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You can give LSA a try. The paper is here http://www.nature.com/nbt/journal/v3.../nbt.3375.html
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Old 06-03-2016, 10:27 AM   #3
kopardev
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Have you tried MyCC (http://www.nature.com/articles/srep24175)
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