Bayesian haplotype-based mutation calling

ClairS - a deep-learning method for long-read somatic small variant calling

A python parser to simplify and build the VCF (Variant Call Format).

An algorithm for recovering haplotypes from metagenomes

Viral quasispecies assembly via maximal clique finding. A method to reconstruct viral haplotypes and detect large insertions and deletions from NGS data.

Intersect multiple VCF files with haplotype awareness

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

Split a BAM file by haplotype support

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Minor Variant Calling and Phasing Tools

A python program that uses ReadBack phased haplotypes in population of samples and returns extended haplotype blocks.

An efficient genetic data imputation pipeline

A collection of WDL bioinformatic workflows to benchmark markers coming from different pipelines using linkage map quality as a diagnosis.

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

Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)

Long sequencing reads classifier

a python program to stitch the ReadBack phased haplotypes in F1 hybrids.

Proteogenomics database-generation tool for protein haplotypes and variants

Create a set of reference-guided multiple-aligned haplotypes or founder sequences from a variant call file and a reference sequence.