Agnieszka Danek1, Sebastian Deorowicz1. 1. Institute of Informatics, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Gliwice, Poland.
Abstract
Motivation: Nowadays, genome sequencing is frequently used in many research centers. In projects, such as the Haplotype Reference Consortium or the Exome Aggregation Consortium, huge databases of genotypes in large populations are determined. Together with the increasing size of these collections, the need for fast and memory frugal ways of representation and searching in them becomes crucial. Results: We present GTC (GenoType Compressor), a novel compressed data structure for representation of huge collections of genetic variation data. It 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 60 000 haplotypes at about 40 million SNPs can be stored in <4 GB, while the queries related to variants are answered in a fraction of a second. Availability and implementation: GTC can be downloaded from https://github.com/refresh-bio/GTC or http://sun.aei.polsl.pl/REFRESH/gtc. Contact: sebastian.deorowicz@polsl.pl. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: Nowadays, genome sequencing is frequently used in many research centers. In projects, such as the Haplotype Reference Consortium or the Exome Aggregation Consortium, huge databases of genotypes in large populations are determined. Together with the increasing size of these collections, the need for fast and memory frugal ways of representation and searching in them becomes crucial. Results: We present GTC (GenoType Compressor), a novel compressed data structure for representation of huge collections of genetic variation data. It 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 60 000 haplotypes at about 40 million SNPs can be stored in <4 GB, while the queries related to variants are answered in a fraction of a second. Availability and implementation: GTC can be downloaded from https://github.com/refresh-bio/GTC or http://sun.aei.polsl.pl/REFRESH/gtc. Contact: sebastian.deorowicz@polsl.pl. Supplementary information: Supplementary data are available at Bioinformatics online.
Authors: Taedong Yun; Helen Li; Pi-Chuan Chang; Michael F Lin; Andrew Carroll; Cory Y McLean Journal: Bioinformatics Date: 2021-01-05 Impact factor: 6.937