CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce…

• UD
  U.S. Department of Energy
• GB
  Great Barrier Reef Foundation
• JG
  Joint Genome Institute
• NS
  Natural Sciences and Engineering Research Council of Canada
• AR
  Australian Research Council

  Awards: DP120103498, DP1093175