FermiKit: assembly-based variant calling for Illumina resequencing data

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: [e-mail]