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How To Determine How Many Strains Of Ecoli In Metagenome

I have a human gut whole genome metagenomics reads. And i must answer the question - is there only one or several ecoli strains in it. How can i do it?

metagenomics
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updated by WANG • WANG • written by zeleniy.spb • zeleniy.spb

3 answers

I have seen recently paper/program that can help you.

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written by Leszek Leszek

You can also find some inspiration in that Banfield's Lab paper:

Morowitz, M. J., Denef, V. J., Costello, E. K., Thomas, B. C., Poroyko, V., Relman, D. A., & Banfield, J. F. (2011). Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proceedings of the National Academy of Sciences of the United States of America, 108(3), 1128–1133. doi:10.1073/pnas.1010992108

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updated by Ram Ram • written by Manu Prestat Manu Prestat

You can use the strain-profiling tool PStrain, it will profile the strains with different strain numbers and choose a reasonable one. So, you can know if there is a mix of strains. Hope it helps.

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written by WANG • WANG

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