vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Language: C++ - Size: 34 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 645 - Forks: 223

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced at: 20 days ago - Pushed at: over 2 years ago - Stars: 156 - Forks: 28

tseemann/nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

Language: Perl - Size: 11.3 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 139 - Forks: 38

single-cell-genetics/cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

Language: C - Size: 890 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 123 - Forks: 11

bioinformatics-centre/BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers

Language: C++ - Size: 1.75 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 83 - Forks: 8

single-cell-genetics/cellSNP

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Language: Python - Size: 224 KB - Last synced at: 19 days ago - Pushed at: almost 3 years ago - Stars: 77 - Forks: 11

iprada/Circle-Map

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

Language: Python - Size: 3.75 MB - Last synced at: 16 days ago - Pushed at: 11 months ago - Stars: 63 - Forks: 19

ACEnglish/kanpig

Kmer Analysis of Pileups for Genotyping

Language: Rust - Size: 5.01 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 27 - Forks: 1

ChaissonLab/danbing-tk

Toolkit for VNTR genotyping and repeat-pan genome graph construction

Language: C++ - Size: 55 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 25 - Forks: 4

cbg-ethz/BnpC

Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates

Language: Python - Size: 237 KB - Last synced at: about 1 month ago - Pushed at: 11 months ago - Stars: 20 - Forks: 4

medvedevgroup/vargeno

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Language: C++ - Size: 35.4 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 19 - Forks: 4

teepean/BAM-Analysis-Kit

Language: Forth - Size: 2.18 GB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 18 - Forks: 6

clemgoub/TypeTE

Genotyping of segregating mobile elements insertions

Language: Perl - Size: 62.5 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 18 - Forks: 1

PlantandFoodResearch/MCHap

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

Language: Python - Size: 15.8 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 17 - Forks: 3

Danderson123/Amira

A tool to detect acquired AMR genes directly from long read sequencing data.

Language: Python - Size: 15.3 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 14 - Forks: 2

stjude/indelPost

Python library for simple and complex indels.

Language: C - Size: 1.17 MB - Last synced at: 2 days ago - Pushed at: over 1 year ago - Stars: 13 - Forks: 3

SandraLouise/SVJedi-graph

SV genotyper for long reads with a variation graph

Language: Python - Size: 11.8 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 12 - Forks: 0

transbioZI/Gimpute

An efficient genetic data imputation pipeline

Language: R - Size: 2.93 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 10 - Forks: 4

interpretAMR/AMRgen

The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating genotype-phenotype associations.

Language: R - Size: 7.94 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 5

MDU-PHL/emmtyper Fork of Andre-Tan/EmMAIL

emm Automatic Isolate Labeller

Language: Jupyter Notebook - Size: 1.35 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 9 - Forks: 3

Gregor-Mendel-Institute/SNPmatch

A simple python library to identify the most likely strain from the population

Language: Python - Size: 92.4 MB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 5

AlgoLab/malva

genotyping by Mapping-free ALternate-allele detection of known VAriants

Language: C - Size: 19.4 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 4

klebgenomics/Kleborate-viz

Visualisation application for Klebsiella genotypes generated by Kleborate.

Language: R - Size: 4.8 MB - Last synced at: 10 months ago - Pushed at: about 4 years ago - Stars: 9 - Forks: 2

nf-cmgg/smallvariants

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

Language: Nextflow - Size: 10.9 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 8 - Forks: 2

Sh1ne111/KMERIA

A KMER-based genome-wIde Assocation testing approach on polyploids

Language: C - Size: 16.4 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 8 - Forks: 0

kohyamat/massgenotyping

Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data

Language: Python - Size: 420 KB - Last synced at: 10 months ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 1

phylo42/sherpas

Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences

Language: C++ - Size: 26.1 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 7 - Forks: 3

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 - Size: 6.35 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 0

akikuno/DAJIN

One-step genotyping software using a long-read sequencer

Language: Python - Size: 36.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 2

asylvz/CONGA

CONGA: COpy Number Genotyping in Ancient genomes and low-coverage sequencing data

Language: C - Size: 1.38 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0

FLI_Bioinfo/WGSBAC

Modules for genotyping and characterisation of bacterial isolates utilizing whole-genome-sequencing data

Last synced at: about 2 years ago - Stars: 5 - Forks: 0

imanyass/ShigaPass

An in silico tool to predict Shigella serotypes

Language: Shell - Size: 7.97 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 3

bedapub/HBVouroboros

HBVouroboros automates sequencing-based HBV genotyping and expression profiling

Language: Python - Size: 23.6 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 1

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 - Size: 5.41 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

casanova-lab/GMUSCLE

Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing

Language: Python - Size: 25.7 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 1

AlgoLab/MALVIRUS

A fast and accurate tool for genotyping haploid individuals (such as SARS-CoV-2)

Language: JavaScript - Size: 5.87 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 2

PengJia6/MSHunter 📦

Microsatellite genotyping

Language: Python - Size: 114 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

Grelot/seaConnect--dDocent

GBS workflow using dDocent. This was designed to process GBS data from SEACONNECT project.

Language: Shell - Size: 69.3 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 1

msk-access/genotype_variants

Project to genotype SNV, INDEL and SV.

Language: Python - Size: 185 KB - Last synced at: 12 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 4

jeanlain/STRyper

A macOS application for microsatellite genotyping using capillary sequencing data.

Language: Objective-C - Size: 23 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

tsnorri/panvc3

Variant calling using a pan-genomic reference, version 3

Language: C++ - Size: 1.12 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

dbespiatykh/tblg

A command-line tool to genotype Mycobacterium tuberculosis lineage from a VCF file

Language: Python - Size: 40 KB - Last synced at: 17 days ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

ut-biomet/breedSimulatR

R 📦 providing classes and functions to simulate breeding schemes.

Language: R - Size: 4.35 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

aryarm/VarBench

Benchmarking variant callers for long read data

Language: Python - Size: 105 KB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

alexliyihao/EFIGA_WGS

Implementation of WGS genotyping pipeline for EFIGA FBS FAMILY dataset

Language: Shell - Size: 104 KB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 0 - Forks: 0

petersm3/buildtassel3

Wrapper scripts for TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) and UNEAK (Universal Network Enabled Analysis Kit) v3.0 Genotyping by Sequencing (GBS) analysis pipelines

Language: Shell - Size: 62.5 KB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

NajlaAbassi/ROHStats

🧬 ROHStats: Fast and easy ROH statistics and visualization from PLINK outputs

Language: R - Size: 11.9 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

germinateplatform/germinate-training

Training material for the use of Germinate

Language: SCSS - Size: 20.5 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

liviuspenter/ONT-lineage-tracing

Analyses of Penter, Borji & Nagler et al., Nature Communications 2024

Language: R - Size: 60.4 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

iliapopov17/BI-Workshop-miniProjects

📚Workshop study projects in Bioinformatics Institute 2023-2024

Language: Jupyter Notebook - Size: 18.3 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

oicr-gsi/sample-fingerprinting

workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

Language: WDL - Size: 1.18 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 2

zjwinn/Mapping-of-a-Novel-Major-Effect-Hessian-Fly-Partial-Resistance-Locus-in-Southern-SRWW-LA03136E71

Data repository for the paper of the same name.

Size: 10.1 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

leabact/ddRADseq-for-prokaryota

This project was written as a first step to apply the ddRADSeq genotyping method to prokaryota. This code is made to dertemine, in silico, the couple of enzymes to apply on a given sequence.

Language: Python - Size: 2.49 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

mohamed-malk/Z-care

Graduation Project (2023)

Size: 1.46 GB - Last synced at: 10 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

ahryho/psychoGE

Joint impact of environmental and genetic determinants on the aetiology of stress-related psychiatric disorders.

Language: HTML - Size: 315 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

gokalpcelik/ROHMMCLI

ROHMMCLI - Flexible HMM based homozygosity predictor.

Language: Java - Size: 272 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

datngu/SNP_array_comparison

Running codes and data analysis scripts for SNP array comparison paper

Language: Shell - Size: 1.23 GB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

baneslab/iScanVCFMerge

Python tool to merge cross-species Illumina iScan genotype data with a reference set of genotypes from a pre-existing source.

Language: Python - Size: 261 KB - Last synced at: 20 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

wanyuac/PAMmaker

Pipelines creating allelic presence-absence matrices from SRST2 and ARIBA results

Language: Python - Size: 88.9 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

YogiOnBioinformatics/Joint-Genotyping-2021-2022

Joint Genotyping in MIT Fraenkel Lab with ALS Genomics + 1000 Genomes Data

Language: Jupyter Notebook - Size: 646 KB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

czbiohub/sunbeam_gt-pro

Functional testing for gt-pro for microbial genotyping

Language: Python - Size: 82 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

tseemann/amplikate

📢🎯 Generic typing tool from amplicons and/or in silico PCR

Language: Perl - Size: 129 KB - Last synced at: about 2 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1

pongorlorinc/mcaller

Language: Python - Size: 44.9 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0