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, with Rick Beeloo (Beeloo and Groot Koerkamp 2025):

  SIMD-based approximate string matching

  • Status: done.
  • Search short (10-100, or up to 1kbp) patterns in long texts.
  • Supports ACTG, IUPAC, and ASCII.

• A*PA2, with Pesho Ivanov (Groot Koerkamp and Ivanov 2024; Groot Koerkamp 2024):

  Global pairwise alignment based on SIMD, bitpacking, and band-doubling

  • Reliable, but only supports ACTG input.

• simd-sketch:

  SIMD-based bottom and bucket sketches.

  • Status: basic version done; needs polishing.
  • Builds on seq-hash.

• mim, with Rob Patro (Patro et al. 2025):

  a small auxiliary .mim index alongside .fastx.gz files for multi-threaded decompression.

Tools building on this Link to heading

• Deacon, by Bede Constantinides (Constantinides, Lees, and Crook 2025): Fast read filtering/decontamination. Builds on simd-minimizers.
• Barbell, by Rick Beeloo (Beeloo et al. 2025): Fast demultiplexing. Builds on sassy.

Libraries Link to heading

• pa_types: type definitions for pairwise alignment coordinates, and Cigar utilities.

DNA bitpacking Link to heading

Crates using 2-bit packed sequence representations and SIMD algorithms on top of them. All developed together with Igor Martayan as part of simd-minimizers (Groot Koerkamp and Martayan 2025).

• 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.
  • Supports skipping over ambiguous windows.

Dependency graph Link to heading

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digraph {
barbell -> sassy
barbell -> pa_types
sassy -> pa_types
deacon -> simd_minimizers
deacon -> packed_seq
simd_minimizers -> seq_hash
simd_minimizers -> packed_seq
seq_hash -> packed_seq
simd_sketch -> packed_seq
simd_sketch -> seq_hash
"A*PA2" -> pa_types
}

Data structures Link to heading

• cacheline_ef: Elias-Fano encoding, one cacheline at a time. Part of PtrHash.
• PtrHash (Groot Koerkamp 2025): A fast minimal perfect hash function.

Experimental/incomplete Link to heading

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

References Link to heading