| Title: | XSI - a genotype compression tool for compressive genomics in large biobanks |
| Journal: | Bioinformatics |
| Published: | 24 Jun 2022 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/35748697/ |
| DOI: | https://doi.org/10.1093/bioinformatics/btac413 |
| URL: | https://academic.oup.com/bioinformatics/article-pdf/38/15/3778/45213127/btac413.pdf |
| Citations: | 10 (8 in last 2 years) as of 8 Aug 2024 |
Publication 12328
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Abstract
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.</p>
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.</p>
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.</p>
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.</p>
5 Keywords
- Biological Specimen Banks
- Data Compression
- Genomics
- Genotype
- Software
5 Authors
- Rick Wertenbroek
- Simone Rubinacci
- Ioannis Xenarios
- Yann Thoma
- Olivier Delaneau
1 Application
| Application ID | Title |
|---|---|
| 66995 | Prediction of haplotypes, genotypes, parental-of-origin and applications in biobanks. |
Enabling scientific discoveries that improve human health