bcftools-compatible querying and format conversion for VCF Zarr.

Reference-free profiling of polyploid genomes.

Statistical genetics toolkit.

Python bindings to spoa.

Smart and Accurate Polishing of Phased Haplotypes Integrating Read Enhancements (SAPPHIRE)

R package for wavelet variance and correlation decompositions of genomic signals, averaging across chromosomes (or more generally any set of multiple temporal or spatial signals).

Draws ASCII trees.

This package provides a fast structural variation caller for long-read sequencing data.

Minibwa aligns short reads against a reference genome. It is the successor of bwa-mem with a different algorithm. Minibwa is over three times as fast as the original bwa-mem and twice as fast as bwa-mem2 at comparable accuracy. While minibwa works with accurate long reads, minimap2 is more robust under high error rate.

Copy number variation detection using NGS data

Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.

Inference of ploidy and heterozygosity structure using whole genome sequencing data.

Convert bioinformatics data to Zarr.

SHAPEIT5 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and sequencing data.

Fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool has multi-threading support to afford high performance.

A fast K-mer counter for high-fidelity shotgun datasets.

FastDup is a tool designed to locate and tag duplicate reads in a coordinate-sorted SAM or BAM file. It uses the same core algorithm as Picard MarkDuplicates to produce identical results and utilizes spdlog for logging, with the default level set to 'info'.

phase genomic variants using DNA sequencing reads.

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy.

GCTA (Genome-wide Complex Trait Analysis) is a software package initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been greatly extended for many other analyses of data from genome-wide association studies (GWASs).

This package provides utilities for exploratory analysis of large scale genetic variation data.

pixy is a command-line tool for painlessly computing unbiased estimators of population genetic summary statistics that measure genetic variation within (π, θW, Tajima’s D) and between (dxy, FST) populations from a VCF. In particular, pixy facilitates the use of VCFs containing invariant (monomorphic) sites, which are essential for the correct computation of π and dxy in the face of missing data (i.e. always).