genotyping
There are 3 repositories under genotyping topic.
vcflib / vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Language:C++ 604- Language:C++ 146
tseemann / nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
Language:Perl 131single-cell-genetics / cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells
Language:C 124bioinformatics-centre / BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
Language:C++ 85Pileup biallelic SNPs from single-cell and bulk RNA-seq data
Language:Python 71iprada / Circle-Map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
Language:Python 60ChaissonLab / danbing-tk
Toolkit for VNTR genotyping and repeat-pan genome graph construction
Language:Python 21- Language:Perl 19
medvedevgroup / vargeno
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
Language:C++ 19PlantandFoodResearch / MCHap
Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
Language:Python 18- Language:Forth 18
cbg-ethz / BnpC
Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates
Language:Python 17- Language:C 12
transbioZI / Gimpute
An efficient genetic data imputation pipeline
Language:R 11- Language:Jupyter Notebook 10
- Language:C 9
Gregor-Mendel-Institute / SNPmatch
A simple python library to identify the most likely strain from the population
Language:Python 9klebgenomics / Kleborate-viz
Visualisation application for Klebsiella genotypes generated by Kleborate.
Language:R 9phylo42 / sherpas
Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences
Language:C++ 8SandraLouise / SVJedi-graph
SV genotyper for long reads with a variation graph
Language:Python 8- Language:C 7
kohyamat / massgenotyping
Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data
Language:Python 7- Language:Python 5
- Language:Shell 5
alethere / SmoothDescent
Repository of SmoothDescent R package. Smooth Descent is a map-cleaning algorithm that can calculate identity by descent probabilities and correct genotyping errors based on marker maps.
Language:R 4nf-cmgg / germline
A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
Language:Nextflow 4- kanpigLanguage:Rust 3
biomguler / G-WASPiper
This repository is my collection of pipelines for basic GWAS analysis, written in R to simplify, please cite original tools/approaches referred in the pipelines.
Language:R 3- Language:JavaScript 2
bedapub / HBVouroboros
HBVouroboros automates sequencing-based HBV genotyping and expression profiling
Language:Python 2casanova-lab / GMUSCLE
Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing
Language:Python 2Grelot / seaConnect--dDocent
GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.
Language:Shell 2- Language:Python 2
- STRyper
jeanlain / STRyper
A macOS application for microsatellite genotyping using capillary sequencing data.
Language:Objective-C 1 TeaShull / PhytoBSA
Establishing genotype-phenotype links using Bulk Segregant Analysis of mutations in Plant populations
Language:Python 1
