Lists (4)
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.
Multithreading Library for Brotli, Lizard, LZ4, LZ5, Snappy and Zstandard
A high performance python hash table library that is generally faster and consumes significantly less memory than Python Dictionaries
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