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pairwise-alignment

README.md

Pairwise Alignment Benchmarks

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.

Pinned Loading

  1. pa-types pa-types Public

    Basic types and functions for pairwise alignment.

    Rust 3

  2. pa-generate pa-generate Public

    Generate random sequence pairs to test pairwise aligners

    Rust 1

  3. pa-bench pa-bench Public

    Benchmarking pairwise aligners

    Jupyter Notebook 35 1

Repositories

Showing 10 of 11 repositories
  • pa-bench-paper Public
    pairwise-alignment/pa-bench-paper’s past year of commit activity
    0 0 0 0 Updated Mar 27, 2024
  • pa-bench Public

    Benchmarking pairwise aligners

    pairwise-alignment/pa-bench’s past year of commit activity
    Jupyter Notebook 35 MIT 1 4 0 Updated Mar 25, 2024
  • pa-types Public

    Basic types and functions for pairwise alignment.

    pairwise-alignment/pa-types’s past year of commit activity
    Rust 3 MIT 0 0 0 Updated Mar 22, 2024
  • pa-extend Public
    pairwise-alignment/pa-extend’s past year of commit activity
    Rust 1 0 0 0 Updated Jul 4, 2023
  • ksw2 Public Forked from lh3/ksw2

    Global alignment and alignment extension, with added band doubling

    pairwise-alignment/ksw2’s past year of commit activity
    C 0 24 0 0 Updated Jun 27, 2023
  • rust-wfa2 Public Forked from Daniel-Liu-c0deb0t/rust-wfa2

    Rust binding for WFA2-lib

    pairwise-alignment/rust-wfa2’s past year of commit activity
    Rust 4 MIT 5 0 0 Updated Jun 26, 2023
  • pa-generate Public

    Generate random sequence pairs to test pairwise aligners

    pairwise-alignment/pa-generate’s past year of commit activity
    Rust 1 MIT 0 0 0 Updated May 7, 2023
  • .github Public

    Org readme

    pairwise-alignment/.github’s past year of commit activity
    0 0 0 0 Updated Mar 22, 2023
  • ksw2-sys Public Forked from rchikhi/ksw2-sys

    Rust bindings for ksw2 alignment library

    pairwise-alignment/ksw2-sys’s past year of commit activity
    Rust 0 1 0 0 Updated Feb 8, 2023
  • edlib-rs Public Forked from Daniel-Liu-c0deb0t/edlib-rs

    rust binding to edlib

    pairwise-alignment/edlib-rs’s past year of commit activity
    Rust 0 5 0 0 Updated Jan 11, 2023
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