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

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.https://github.com/lh3/[e-mail].

SUBMITTER: Li H 

PROVIDER: S-EPMC4757955 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature