Daniel Liu

seqproc: An efficient, flexible, and concise tool for sequence geometry description and transformation

seqproc is a tool that efficiently compiles sequence-geometry descriptions into execution graphs, outperforming existing tools in speed and memory usage for single-cell RNA-sequencing protocols.

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.

Best: A Tool for Characterizing Sequencing Errors

The paper introduces a tool called best for efficiently quantifying sequencing errors in aligned reads and shows it is 16 times faster than existing methods.

Block aligner: fast and flexible pairwise sequence alignment with SIMD-accelerated adaptive blocks

The paper introduces a new sequence alignment algorithm called block aligner that is faster than existing methods while maintaining accuracy on realistic datasets.

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers

The paper introduces a new method for efficiently deduplicating reads using Unique Molecular Identifiers (UMIs) by optimizing data structures and algorithms.

Fuzzysplit: Demultiplexing and Trimming Sequenced DNA With a Declarative Language

Fuzzysplit is a demultiplexing and trimming tool that uses a declarative language to describe sequence schematics, offering adaptability and comparable matching accuracy to existing tools.