CoverM: read alignment statistics for metagenomics

SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and…

• NS
  National Science Foundation

  Award: DE-AC02-05CH11231
• UD
  U.S. Department of Energy

  Awards: -AC02-05CH11231, 05CH11231, DE-SC0010580, DE-SC0004632, AC02-05CH11231, DE-AC02, DE-AC02-05CH11231, DE-SC0016440, DE-AC02-
• JG
  Joint Genome Institute

  Awards: DE-AC02-05CH11231, AC02-05CH11231
• FD
  Fundação de Amparo à Pesquisa do Estado de São Paulo

  Award: 2018/04240-0
• OO
  Office of Science

  Awards: AC02-05CH11231, -AC02-05CH11231, DE-AC02
• BA
  Biological and Environmental Research

  Awards: DE-SC0016440, 05CH11231, DE-SC0010580, DE-SC0004632, DE-AC02-05CH11231, AC02-05CH11231