genotyping
There are 60 repositories under genotyping topic.
vcflib/vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
Illumina/paragraph
Graph realignment tools for structural variants
tseemann/nullarbor
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
single-cell-genetics/cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells
bioinformatics-centre/BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
single-cell-genetics/cellSNP
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
iprada/Circle-Map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
ChaissonLab/danbing-tk
Toolkit for VNTR genotyping and repeat-pan genome graph construction
clemgoub/TypeTE
Genotyping of segregating mobile elements insertions
medvedevgroup/vargeno
Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.
PlantandFoodResearch/MCHap
Polyploid micro-haplotype assembly using Markov chain Monte Carlo simulation.
cbg-ethz/BnpC
Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates
stjude/indelPost
Python library for simple and complex indels.
transbioZI/Gimpute
An efficient genetic data imputation pipeline
MDU-PHL/emmtyper
emm Automatic Isolate Labeller
AlgoLab/malva
genotyping by Mapping-free ALternate-allele detection of known VAriants
Gregor-Mendel-Institute/SNPmatch
A simple python library to identify the most likely strain from the population
klebgenomics/Kleborate-viz
Visualisation application for Klebsiella genotypes generated by Kleborate.
phylo42/sherpas
Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences
SandraLouise/SVJedi-graph
SV genotyper for long reads with a variation graph
asylvz/CONGA
CONGA: COpy Number Genotyping in Ancient genomes and low-coverage sequencing data
kohyamat/massgenotyping
Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data
akikuno/DAJIN
One-step genotyping software using a long-read sequencer
imanyass/ShigaPass
An in silico tool to predict Shigella serotypes
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.
nf-cmgg/germline
A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
ACEnglish/kanpig
Kmer Analysis of Pileups for Genotyping
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.
AlgoLab/MALVIRUS
A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)
bedapub/HBVouroboros
HBVouroboros automates sequencing-based HBV genotyping and expression profiling
casanova-lab/GMUSCLE
Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing
Grelot/seaConnect--dDocent
GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.
PengJia6/MSHunter
Microsatellite genotyping
jeanlain/STRyper
A macOS application for microsatellite genotyping using capillary sequencing data.
TeaShull/PhytoBSA
Establishing genotype-phenotype links using Bulk Segregant Analysis of mutations in Plant populations