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Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440. Epub 2015 Jul 27.

FermiKit: assembly-based variant calling for Illumina resequencing data.

Author information

1
Genomics Platform, Broad Institute, Cambridge, MA 02142, USA.

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.

AVAILABILITY AND IMPLEMENTATION:

https://github.com/lh3/fermikit

CONTACT:

hengli@broadinstitute.org.

PMID:
26220959
PMCID:
PMC4757955
DOI:
10.1093/bioinformatics/btv440
[Indexed for MEDLINE]
Free PMC Article

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