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Method: An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
- Stephen Nayfach,
- Beltran Rodriguez-Mueller,
- Nandita Garud,
- and Katherine S. Pollard
Genome Res. November 2016 26: 1612-1625; Published in Advance October 18, 2016, doi:10.1101/gr.201863.115
...into a pathogen (Snitkin et al. 2011), or lead to outbreaks of highly virulent strains (Rasko et al. 2011). Metagenomic shotgun sequencing has the potential to shed light onto strain-level heterogeneity among bacterial s within and between microbial communities, yielding a genomic resolution not achievable...
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Resource: Using populations of human and microbial genomes for organism detection in metagenomes
- Sasha K. Ames,
- Shea N. Gardner,
- Jose Manuel Marti,
- Tom R. Slezak,
- Maya B. Gokhale,
- and Jonathan E. Allen
Genome Res. July 2015 25: 1056-1067; Published in Advance April 29, 2015, doi:10.1101/gr.184879.114
...Microbiome Project (HMP) samples (Martin et al. 2012) used a microbial reference database totaling 7.3 gigabases (Gb), which represents only a small fraction of the sequenced microbial strains available. In the case of SURPI, although a 42-Gb GenBank NT database is searched, a best first match approach...
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