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arXiv · 1504.06574

FermiKit: assembly-based variant calling for Illumina resequencing data

Heng Li
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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

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Heng Li. 2015-04-24. FermiKit: assembly-based variant calling for Illumina resequencing data. https://arxiv.org/abs/1504.06574

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