FermiKit: assembly-based variant calling for Illumina resequencing data

TL;DR

FermiKit is an assembly-based pipeline for variant calling in Illumina resequencing data that assembles reads de novo and maps the assembly to identify SNPs, INDELs, and SVs efficiently and accurately.

Contribution

It introduces a novel assembly-based approach for variant calling that maintains high accuracy while reducing raw data complexity.

Findings

Assembles 30-fold human genome in about one day on a 16-core server.

Calls variants in half an hour with accuracy comparable to existing methods.

Retains most original information despite data reduction.

Abstract

Summary: FermiKit is a variant calling pipeline for Illumina 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. Availability and implementation: https://github.com/lh3/fermikit Contact: hengli@broadinstitute.org