  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
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