Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data.
In: Bioinformatics, Jg. 37 (2021-08-01), Heft 15, S. 2121-2125
Online
academicJournal
Zugriff:
Motivation Pairwise comparison problems arise in many areas of science. In genomics, datasets are already large and getting larger, and so operations that require pairwise comparisons—either on pairs of SNPs or pairs of individuals—are extremely computationally challenging. We propose a generic algorithm for addressing pairwise comparison problems that breaks a large problem (of order n 2 comparisons) into multiple smaller ones (each of order n comparisons), allowing for massive parallelization. Results We demonstrated that this approach is very efficient for calling identical by descent (IBD) segments between all pairs of individuals in the UK Biobank dataset, with a 250-fold savings in time and 750-fold savings in memory over the standard approach to detecting such segments across the full dataset. This efficiency should extend to other methods of IBD calling and, more generally, to other pairwise comparison tasks in genomics or other areas of science. Availability and Implementation A GitHub page is available at https://github.com/emmanuelsapin with the code to generate data needed for the implementation [ABSTRACT FROM AUTHOR]
Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Titel: |
Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data.
|
---|---|
Autor/in / Beteiligte Person: | Sapin, Emmanuel ; Keller, Matthew C |
Link: | |
Zeitschrift: | Bioinformatics, Jg. 37 (2021-08-01), Heft 15, S. 2121-2125 |
Veröffentlichung: | 2021 |
Medientyp: | academicJournal |
ISSN: | 1367-4803 (print) |
DOI: | 10.1093/bioinformatics/btab084 |
Schlagwort: |
|
Sonstiges: |
|