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Published on: June 21, 2018
XSI-a genotype compression tool for compressive genomics in large biobanks
Rick Wertenbroek1,2, Simone Rubinacci2, Ioannis Xenarios2
1School of Management and Engineering Vaud (HEIG-VD), HES-SO University of Applied Sciences and Arts Western Switzerland, Yverdon-les-Bains 1401, Switzerland.
Motivation:
Generation of genotype data has been growing exponentially over the last decade. With the large size of recent datasets comes a storage and computational burden with ever increasing costs. To reduce this burden, we propose XSI, a file format with reduced storage footprint that also allows computation on the compressed data and we show how this can improve future analyses.
Results:
We show that xSqueezeIt (XSI) allows for a file size reduction of 4-20× compared with compressed BCF and demonstrate its potential for 'compressive genomics' on the UK Biobank whole-genome sequencing genotypes with 8× faster loading times, 5× faster run of homozygozity computation, 30× faster dot products computation and 280× faster allele counts.
Availability And Implementation:
The XSI file format specifications, API and command line tool are released under open-source (MIT) license and are available at https://github.com/rwk-unil/xSqueezeIt.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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