DeCGR: an interactive toolkit for deciphering complex genomic rearrangements from Hi-C data
Junping Li, Minghui Sun, Yusen Ye, Lin Gao · 2024
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Description
Junping Li and co-authors present a software toolkit for reading complex genome rearrangements from contact maps, in a 2024 paper. Such rearrangements reshape how DNA folds, and they show up as odd blocks in maps made by a capture method that logs which DNA parts touch. Those blocks reveal where fragments sit and which way they face. No hands-on graphics tool existed for turning blocks into full rearrangement calls.
Their Python toolkit runs in four parts. One filters out simple rearrangements and logs break points. A second assembles the complex ones and draws the process as it goes. A third checks each call by faking a map from it and comparing that map with the real one. A fourth rebuilds the map so users can see the fold change directly. The authors aim the tool at biologists who work from contact maps daily.
Catalog record
| CREATOR | Junping Li, Minghui Sun, Yusen Ye, Lin Gao |
|---|---|
| YEAR | 2024 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 38 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |