1. Directory
  2. Genomics
  3. Genome annotation
  4. Repetitive DNA
Join community Sign in
By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.

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:
Command line interface
Restrictions to use:
Biological technology:
Operating system:
Computer skills:
View all reviews

0 user review

No review has been posted.

View all issues

0 issue

No open issue.


  • Heng Li <hengli at broadinstitute.org>


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

59 related tools