SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings
Joshua Rubin, Jan van Waaij, Louis Kraft, Jouni Sirén, Peter Wad Sackett, Gabriel Renaud · 2025
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Description
Joshua Rubin and co-authors present SAFARI, a tool for ancient DNA alignment in a 2025 paper. Ancient DNA is short and chemically damaged, which warps its letters. Standard alignment against one reference genome adds bias.
Pangenome graphs reduce that bias by holding known variation. Damage patterns still distort short fossil reads, though. Their index encodes bases by chemical family, purine or pyrimidine. Damage that swaps within a family stops confusing the matcher. The RYmer index builds on the common minimizer idea. Readers in genomics get a damage-aware way to place very old DNA.
Catalog record
| CREATOR | Joshua Rubin, Jan van Waaij, Louis Kraft, Jouni Sirén, Peter Wad Sackett, Gabriel Renaud |
|---|---|
| YEAR | 2025 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 64 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |