Stars
Implementations of SIMD instruction sets for systems which don't natively support them.
A high-performance immutable mapping type for Python.
Python library for handling efficiently sorted integer sets.
NCLS. Basically a static interval-tree that is silly fast for both construction and lookups. Deprecated but maintained.
A high performance python hash table library that is generally faster and consumes significantly less memory than Python Dictionaries
Multithreading Library for Brotli, Lizard, LZ4, LZ5, Snappy and Zstandard
Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
A fast K-mer counter for high-fidelity shotgun datasets
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.
A reimplementation of the WaveFront Alignment algorithm at low memory
Identifies duplicate reads. This tool locates and tags duplicate reads in a coordinate ordered SAM or BAM file.
An extension to the wavefront algorithm that generalizes it to work on directed acyclic sequence graphs