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  2. High-throughput sequencing
  3. Whole-genome sequencing
  4. Germline SNP detection
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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 (INDELs) and structural variations (SVs). FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85GB 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.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Biological technology:
Illumina
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Heng Li <hengli at broadinstitute.org>

Institution(s)

Broad Institute, 75 Ames Street, Cambridge, MA 02142, USA

Funding source(s)

NHGRI U54HG003037; NIH GM100233

  • (Li, 2015) FermiKit: assembly-based variant calling for Illumina resequencing data. Bioinformatics.
    PMID: 26220959
  • (Neuman et al., 2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in bioinformatics.
    PMID: 22707752

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