GIN-TONIC: non-hierarchical full-text indexing for graph genomes
Ünsal Öztürk, Marco Mattavelli, Paolo Ribeca · 2024
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Description
Ünsal Öztürk, Marco Mattavelli, and Paolo Ribeca presented a new tool for searching graph genomes in two thousand twenty-four. Their tool is called GIN-TONIC. It treats a whole graph as one object, rather than in layers, and it can index graphs that stand for pangenomes or sets of gene transcripts.
The paper shows that the tool can find exact text matches across all paths in a graph, even when those paths are far too many to list. Tests on human-scale data show speed close to a simple linear index, with strong scaling. Code and test data are shared on GitHub for others to use.
Catalog record
| CREATOR | Ünsal Öztürk, Marco Mattavelli, Paolo Ribeca |
|---|---|
| YEAR | 2024 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 78 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |