A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing.

ABSTRACT: Microbes live in complex communities that are of major importance for environmental ecology, public health, and animal physiology and pathology. Short-read metagenomic shotgun sequencing is currently the state-of-the-art technique for exploring these communities. With the aid of metagenomics, our understanding of the microbiome is moving from composition toward functionality, even down to the genetic variant level. While the exploration of single-nucleotide variation in a genome is a standard procedure in genomics, and many sophisticated tools exist to perform this task, identification of genetic variation in metagenomes remains challenging. Major factors that hamper the widespread application of variant-calling analysis include low-depth sequencing of individual genomes (which is especial

SUBMITTER: Andreu-Sanchez S 

PROVIDER: S-EPMC8141913 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature