Bcmap: fast alignment-free barcode mapping for linked-read sequencing data

Abstract

The bottleneck for genome analysis will soon shift from sequencing cost to computationally expensive read alignment. Here, we propose to circumvent full read alignment computation on linked-read sequencing data when only portions of the genome are of interest. Our novel barcode mapping approach "bcmap" indexes and places barcoded read sets on the reference genome, thereafter allowing the extraction of reads originating from genomic regions of interest directly from FASTQ files. We demonstrate that bcmap is accurate and an order of magnitude faster than full read alignment. As example application, we use bcmap to locally assemble a known variant region.