tools for working with genome variation graphs

31 bioinformatics utilities in a trenchcoat

a C++ API of htslib to be easily integrated and safely used. More importantly, it can be callled seamlessly in R/Python/Julia etc.

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

Locus Overlap Analysis: Enrichment of Genomic Ranges

R wrapper for htslib for high-throughput sequence analysis

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

a wee tool for random access into BGZF files.

The Julia Programming Language

High-level functions for parallel programming with Rcpp

Multiscale representation of genomic signals

DSRC - DNA Sequence Reads Compressor

Nonparametric Bayesian Inference for Sequential Data. Includes state-of-the-art MCMC inference for Beta process Hidden Markov Models (BP-HMM). Implemented in Matlab.

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads