Bayesian haplotype-based mutation calling
ClairS: a deep-learning method for long-read tumor–normal pair 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.
Recomb-Mix: a local ancestry inference tool
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.
A long-read somatic phasing software for tumor-only sequencing
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
Proteogenomics database-generation tool for protein haplotypes and variants
A long-read somatic phasing software for tumor-normal paired sequencing
Smart and Accurate Polishing of Phased Haplotypes Integrating Read Enhancements (SAPPHIRE)
A collection of WDL bioinformatic workflows to benchmark markers coming from different pipelines using linkage map quality as a diagnosis.
Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)
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