Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3-5 Kb inserts. Pilon significantly improves draft…

• UD
  U.S. Department of Health and Human Services

  Award: HHSN272200900018C
• BI
  Broad Institute

  Award: U54HG003067
• VR
  Vlaamse regering
• NI
  National Institutes of Health

  Awards: U54HG003067, HHSN272200900018C
• NH
  National Human Genome Research Institute

  Award: U54HG003067
• NI
  National Institute of Allergy and Infectious Diseases

  Award: HHSN272200900018C