Ragnar Groot Koerkamp

Sassy: Fuzzy Searching DNA Sequences using SIMD

Sassy is a fast approximate string matching tool for DNA sequences, achieving significant speedups over existing methods for small error tolerances and applied to CRISPR off-target detection.

Sassy2: Batch Searching of Short DNA Patterns

Sassy2 improves short DNA pattern searching by optimizing SIMD parallelism and filtering, achieving significant speedups over previous methods.

mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing

The paper introduces mim, a lightweight index to accelerate parallel parsing of gzipped FASTQ files with minimal overhead and storage.

Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data

Barbell improves demultiplexing of Nanopore sequencing data by addressing barcode artifacts, reducing trimming errors and barcode bleeding.

The open-closed mod-minimizer algorithm

The paper introduces the open-closed mod-minimizer, a method that improves k-mer sampling density for all k values compared to existing methods.

SimdMinimizers: Computing random minimizers, fast

The paper introduces a fast library for computing random minimizers using SIMD instructions, achieving significant speed improvements over existing methods.

A near-tight lower bound on the density of forward sampling schemes

The paper establishes a near-tight lower bound on the density of forward sampling schemes and shows existing schemes are closer to optimal than previously thought.

The mod-minimizer: a simple and efficient sampling algorithm for long k-mers

The paper introduces the mod-minimizer, a sampling algorithm that improves k-mer density over existing methods for large k and w, achieving optimal density as k approaches infinity.

A*PA2: up to 20 times faster exact global alignment

A*PA2 is an exact global aligner that achieves up to 20x faster runtime than existing methods on long reads with high divergence.

Exact global alignment using A* with chaining seed heuristic and match pruning

This paper introduces an exact global alignment algorithm using A* with chaining seed heuristic and match pruning, achieving near-linear runtime and significant speedups over existing methods.

Aligning Distant Sequences to Graphs using Long Seed Sketches

The paper introduces a long seed sketch method for sequence-to-graph alignment, improving time-accuracy trade-offs in high mutation rate scenarios.