FermiKit: assembly-based variant calling for Illumina resequencing data

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-geno...

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Bibliographic Details
Published inBioinformatics (Oxford, England) Vol. 31; no. 22; pp. 3694 - 3696
Main Author Li, Heng
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.11.2015
Subjects
Algorithms
Applications Notes
Base Pairing - genetics
Genome, Human
Humans
INDEL Mutation - genetics
Polymorphism, Single Nucleotide - genetics
Sequence Analysis, DNA - methods
Sequence Deletion
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Summary: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
Bibliography:Associate Editor: Inanc Birol
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btv440