Article ; Online: GBZ file format for pangenome graphs.
Bioinformatics (Oxford, England)
2022 Volume 38, Issue 22, Page(s) 5012–5018
Abstract: Motivation: Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data ... ...
Abstract | Motivation: Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space efficiently. Results: We propose the GBZ file format based on data structures used in the Giraffe short-read aligner. The format provides good compression, and the files can be efficiently loaded into in-memory data structures. We provide compression and decompression tools and libraries for using GBZ graphs, and we show that they can be efficiently used on a variety of systems. Availability and implementation: C++ and Rust implementations are available at https://github.com/jltsiren/gbwtgraph and https://github.com/jltsiren/gbwt-rs, respectively. Supplementary information: Supplementary data are available at Bioinformatics online. |
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MeSH term(s) | High-Throughput Nucleotide Sequencing ; Software ; Data Compression ; Libraries |
Language | English |
Publishing date | 2022-09-30 |
Publishing country | England |
Document type | Journal Article ; Research Support, N.I.H., Extramural |
ZDB-ID | 1422668-6 |
ISSN | 1367-4811 ; 1367-4803 |
ISSN (online) | 1367-4811 |
ISSN | 1367-4803 |
DOI | 10.1093/bioinformatics/btac656 |
Database | MEDical Literature Analysis and Retrieval System OnLINE |
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