C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Graph realignment tools for structural variants

Efficient genotyping bi-allelic SNPs on single cells

💾 📃 "Reads to report" for public health and clinical microbiology

A method for variant graph genotyping based on exact alignment of k-mers

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

A KMER-based genome-wIde Assocation testing approach on polyploids

Kmer Analysis of Pileups for Genotyping

Toolkit for VNTR genotyping and repeat-pan genome graph construction

A tool to detect acquired AMR genes directly from long read sequencing data.

EcoliTyper: A species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli. Perfect for clinical microbiology, outbreak investigations, and genomic research.

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates

The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating genotype-phenotype associations.

Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.

tandemtwister: Tandem repeat genotyping tool

Genotyping of segregating mobile elements insertions

SV genotyper for long reads with a variation graph