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.
© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.