FermiKit: assembly-based variant calling for Illumina resequencing data

UNLABELLED 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. AVAILABILITY AND IMPLEMENTATION https://github.com/lh3/fermikit CONTACT hengli@broadinstitute.org.

• Publication year

  2015

• Venue

  Bioinform.

• Publication date

  2015-04-24

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btv440arXiv 1504.06574PMID 26220959PMCID PMC4757955
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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