Identifying Bacterial Strains from Sequencing Data
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Environmental and clinical settings can host a wide variety of both bacterial species and strains in a single colony but accurate identification of the organisms is difficult. We describe BIB, a probabilistic method for estimating the relative abundances of species or strains contained in mixed samples analyzed by short read high-throughput sequencing. By grouping closely related strains together in clusters, the BIB pipeline is capable of estimating the relative abundances of the clusters contained in a sequencing sample.
Key wordsBacteria Strain identification Abundance estimation Metagenomics Probabilistic modelling
This work was supported by the Academy of Finland [259440 to A.H., 251170 to J.C.].
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