Danek, 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

GTC: An Attempt To Maintenance Of Huge Genome Collections Compressed

MotivationO_ST_ABSResultsC_ST_ABSWe present GTC, a novel compressed data structure for representation of huge collections of genetic variation data. GTC significantly outperforms existing solutions in terms of compression ratio and time of answering various types of queries. We show that the largest of publicly available database of about 60 thousand haplotypes at about 40 million SNPs can be stored in less than 4 Gbytes, while the queries related to variants are answered in a fraction of a second.\n\nAvailabilityGTC can be downloaded from https://github.com/refresh-bio/GTC or http://sun.aei.polsl.pl/REFRESH/GTC.\n\nContactsebastian.deorowicz@polsl.pl

bioinformatics↗