UCSC Genome Browser source tree. Stable branch: "beta".

Construction and utility of BWT for DNA string sets

PxBLAT: An Efficient and Ergonomic Python Binding Library for BLAT

TransAnnot - a fast transcriptome annotation pipeline

C library for high-throughput sequencing data formats

Constructing a pangenome gene graph

All UCSC Genome Browser source code that is under an open source license, mostly file format converters, command line tools and C libraries. A subset of the "kent" repo, updated every three weeks.

Extraction of genomic background set of DNA sequences for a given foreground set of sequences for subsequent de novo motif discovery

Foldseek enables fast and sensitive comparisons of large structure sets.

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

The fastest VCF/BCF parser in R https://doi.org/10.1093/bioinformatics/btae049

MMseqs2: ultra fast and sensitive search and clustering suite

♥ Essential Functions for DNA Manipulation

Software for monitoring metagenomes using nanopore sequencing reads

Alignment-free simulation, computation, and visualization of Low-compexity regions in biological data

A python library for accessing 2bit files

Better Alignments with Translated HMMER

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Unsafe low-level Rust bindings for the ViennaRNA package.