This organisation hosts a number of repositories related to benchmarking global pairwise aligners. The main repo is pa-bench, which contains more info.

Feel free to reach out to get involved!

Repositories (planned to be) hosted here:

• pa-types: Rust library with core types.
• pa-generate: A crate to generate semi-random sequence pairs to test aligners on.
• Consistent Rust bindings for popular pairwise aligners.
  • WFA
  • Edlib
  • Triple-accel
  • Block aligher
  • A*PA
  • KSW2
  • Parasail
  • SeqAn
  • DAligner
  • Bitpal
  • Gaba
• pa-bench: binaries to benchmark pairwise aligners.
• A thorough benchmark of existing aligners analysing:
  • random and real data,
  • sequence length from 100 to 1M,
  • error rate from 0.1% to 20%,
  • unit, linear, and (double) affine cost models.

Our high level plan is discussed in this doc.

Note: library names start with pa- so that we can publish them to crates.io under the same name.