An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria
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An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.
We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into...
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تاریخ انتشار 2016