title: FermiKit: assembly-based variant calling for Illumina resequencing data.
abstract: FermiKit is a variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions and structural variations. FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85 GB RAM at the peak, and calls variants in half an hour to an accuracy comparable to the current practice. FermiKit assembly is a reduced representation of raw data while retaining most of the original information.
  
  
  METHODS
  https://github.com/lh3/fermikit
  
  
  BACKGROUND
  hengli@broadinstitute.org.
authors.affiliation: Genomics Platform, Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Li
mesh_terms: D000465:Algorithms; D020029:Base Pairing / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D054643:INDEL Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion