Software

For all my projects, feel free to create issues and/or reach out for help in using them. My work is more on algorithm development rather than direct bioinformatics applications, and so I appreciate getting in contact with potential users :)

Tools Link to heading

• Sassy: SIMD-based approximate string matching
  • Status: done.
  • Search short (10-100, or up to 1kbp) patterns in long texts.
  • Supports ACTG, IUPAC, and ASCII.
• simd-sketch: SIMD-based bottom and bucket sketches.
  • Status: basic version done; could use polishing.
  • Builds on seq-hash.
• A*PA2: Global pairwise alignment based on SIMD, bitpacking, and band-doubling
  • Reliable, but only supports ACTG input.

Bitpacked DNA crates Link to heading

Crates using 2-bit packed sequence representations and SIMD algorithms on top of them.

• packed_seq: Slowly growing library for managing 2-bit encoded ACTG DNA sequences.
  • Also supports 2+1 bit encoding to indicate ambiguous (N) characters.
• seq-hash: Streams over all nt-hashes (or other hashes) of a packed sequences.
• simd-minimizers: compute minimizers of a sequence.
  • Support skipping over ambiguous windows.

Further libraries Link to heading

• cacheline_ef: Elias-Fano encoding, one cacheline at a time.
• PtrHash: A fast minimal perfect hash function.

Experimental/incomplete Link to heading

• Minimizers: reference implementations and experiments for minimizer and sampling schemes.
• sshahs-rs: quick but incomplete reimplementation of SSHash.
• suffix array searching: static search trees are faster than binary search.