Sparse allele vectors and the savvy software suite
Abstract Summary The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been develope...
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| Vydané v: | Bioinformatics (Oxford, England) Ročník 37; číslo 22; s. 4248 - 4250 |
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| Hlavní autori: | , , , |
| Médium: | Journal Article |
| Jazyk: | English |
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England
Oxford University Press
18.11.2021
Oxford Publishing Limited (England) |
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| ISSN: | 1367-4803, 1367-4811, 1367-4811 |
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| Abstract | Abstract
Summary
The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software.
Availability and implementation
https://github.com/statgen/savvy.
Supplementary information
Supplementary data are available at Bioinformatics online. |
|---|---|
| AbstractList | The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software. Availability and implementation https://github.com/statgen/savvy. Supplementary information Supplementary data are available at Bioinformatics online. The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software.SUMMARYThe sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software.https://github.com/statgen/savvy.AVAILABILITY AND IMPLEMENTATIONhttps://github.com/statgen/savvy.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. Abstract Summary The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software. Availability and implementation https://github.com/statgen/savvy. Supplementary information Supplementary data are available at Bioinformatics online. The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association analysis by leveraging techniques for fast deserialization of data into computer memory. A command line interface has been developed to complement the storage format and supports basic features like importing, exporting and subsetting. Additionally, a C++ programming API is available allowing for easy integration into analysis software. https://github.com/statgen/savvy. Supplementary data are available at Bioinformatics online. |
| Author | LeFaive, Jonathon Smith, Albert V Abecasis, Gonçalo Kang, Hyun Min |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33989384$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1038/s41586-018-0579-z 10.1186/s13742-015-0047-8 10.1093/bioinformatics/btq671 10.1093/bioinformatics/btu014 10.1038/nmeth.3654 10.1093/bioinformatics/btx145 10.1093/bioinformatics/btr509 10.1093/bioinformatics/btv613 10.1101/gr.107524.110 10.1038/s41586-021-03205-y |
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| Copyright | The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2021 The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com |
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| DOI | 10.1093/bioinformatics/btab378 |
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The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput... The sparse allele vectors file format is an efficient storage format for large-scale DNA variation data and is designed for high throughput association... |
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| SubjectTerms | Alleles Applications Notes Association analysis Availability Bioinformatics Data analysis Format Line interfaces Software Software packages |
| Title | Sparse allele vectors and the savvy software suite |
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