Daniel Liu's repositories
block-aligner
SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.
triple_accel
Rust edit distance routines accelerated using SIMD. Supports fast Hamming, Levenshtein, restricted Damerau-Levenshtein, etc. distance calculations and string search.
UMICollapse
Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
Adversarial-point-perturbations-on-3D-objects
New distributional and shape attacks on neural networks that process 3D point cloud data.
ANTISEQUENCE
Rust library for processing sequencing reads.
simple-saca
Hardware go brrr bounded context suffix array construction algorithm
Java-Fuzzy-Search
A general, multi-threaded fuzzy searching language, called fuzzysplit, that is built on top of a fast and flexible Java fuzzy search library. Can be applied to demultiplex and trim DNA.
diff-align
Differentiable position-specific probability matrix alignment.
consulting
Consulting website.
diff-bench-paper
Edits to the supplementary data of the difference recurrence alignment paper.
libsais-rs
rust bindings to libsais
simulate-seqs
Simulate sequences.
adaptivebandbench
Benchmark on adaptive banded algorithm
arewebioyet.github.io
Rust in bioinformatics and computational biology
Daniel-Liu-c0deb0t.github.io
My personal website.
FLAMAnalysis
Data Analysis For FLAM-Seq Third Generation RNA Sequencing
gccontent-benchmark
Benchmarking different languages for a simple bioinformatics task (Counting the GC fraction of DNA in a FASTA file)
parasailors-new
Rust bindings to parasail, a SIMD-accelerated pairwise sequence alignment library.
rust-alignbench
Pairwise nucleotide alignment benchmark of Rust bindings
rust-bk-tree
A BK-tree implementation in Rust.