Gudys, A. | Search bioRxiv

bioRxiv2018

Kmer-db: instant evolutionary distance estimation

SummaryKmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40,715 pathogens in less than 4 minutes (on a modern workstation), 44 times faster than Mash, its main competitor.\n\nAvailability and Implementationhttps://github.com/refresh-bio/kmer-db\n\nContactsebastian.deorowicz@polsl.pl\n\nSupplementary informationSupplementary data are available at publishers Web site

bioinformatics↗

bioRxiv2017

Whisper: Read sorting allows robust mapping of sequencing data

MotivationMapping reads to a reference genome is often the first step in a sequencing data analysis pipeline. Mistakes made at this computationally challenging stage cannot be recovered easily.\n\nResultsWe present Whisper, an accurate and high-performant mapping tool, based on the idea of sorting reads and then mapping them against suffix arrays for the reference genome and its reverse complement. Employing task and data parallelism as well as storing temporary data on disk result in superior time efficiency at reasonable memory requirements. Whisper excels at large NGS read collections, in particular Illumina reads with typical WGS coverage. The experiments with real data indicate that our solution works in about 15% of the time needed by the well-known Bowtie2 and BWA-MEM tools at a comparable accuracy (validated in variant calling pipeline).\n\nAvailabilityWhisper is available for free from https://github.com/refresh-bio/Whisper or http://sun.aei.polsl.pl/REFRESH/Whisper/\n\nContactsebastian.deorowicz@polsl.pl\n\nSupplementary informationSupplementary data are available at publisher Web site.

bioinformatics↗