vcflib/vcflib

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

Language: C++ - Size: 32.9 MB - Last synced: about 6 hours ago - Pushed: 14 days ago - Stars: 599 - Forks: 219

cbg-ethz/BnpC

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

Language: Python - Size: 230 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 17 - Forks: 4

gauravcodepro/genotyping-platform

a custom function which can be used to prepare the files for the genotyping or the sequencing. You can specify the path and the fasta files and mark them according to the desired condition for the genotyping or sequencing

Language: Python - Size: 19.5 KB - Last synced: 5 days ago - Pushed: 10 days 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: 9 days ago - Pushed: 25 days 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: 10 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

jeanlain/STRyper

A macOS application for microsatellite genotyping using capillary sequencing data.

Language: Objective-C - Size: 25.8 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 1 - Forks: 0

imanyass/ShigaPass

An in silico tool to predict Shigella serotypes

Language: Shell - Size: 7.97 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 4 - Forks: 3

nf-cmgg/germline

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

Language: Nextflow - Size: 8.53 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 4 - Forks: 1

iliapopov17/BI-Workshop-miniProjects

Repository for workshop study projects in Bioinformatics Institute 2023-2024

Language: Jupyter Notebook - Size: 16.1 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

single-cell-genetics/cellSNP

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

Language: Python - Size: 224 KB - Last synced: 22 days ago - Pushed: almost 2 years ago - Stars: 71 - Forks: 10

oicr-gsi/sample-fingerprinting

workflow that generates genotype fingerprints consumed by SampleFingerprinting workflow

Language: wdl - Size: 1.18 MB - Last synced: 28 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 2

single-cell-genetics/cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

Language: C - Size: 824 KB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 115 - 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: 22 days ago - Pushed: almost 2 years ago - Stars: 60 - Forks: 17

tsnorri/panvc3

Variant calling using a pan-genomic reference, version 3

Language: C++ - Size: 832 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

SandraLouise/SVJedi-graph

SV genotyper for long reads with a variation graph

Language: Python - Size: 11.8 MB - Last synced: 2 months ago - Pushed: 7 months ago - Stars: 8 - Forks: 0

Illumina/paragraph

Graph realignment tools for structural variants

Language: C++ - Size: 30.8 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 143 - Forks: 28

asylvz/CONGA

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

Language: C - Size: 1.38 MB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 5 - Forks: 0

msk-access/genotype_variants

Project to genotype SNV, INDEL and SV.

Language: Python - Size: 164 KB - Last synced: 28 days ago - Pushed: 3 months ago - Stars: 1 - Forks: 4

AlgoLab/malva

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

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

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: 3 months ago - Pushed: 3 months ago - Stars: 2 - 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: 254 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

PlantandFoodResearch/MCHap

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

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

kohyamat/massgenotyping

Python package for microsatellite genotyping from highly multiplexed amplicon sequencing data

Language: Python - Size: 420 KB - Last synced: 5 days ago - Pushed: 3 months ago - Stars: 7 - Forks: 1

bioinformatics-centre/BayesTyper

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

Language: C++ - Size: 1.75 MB - Last synced: 5 months ago - Pushed: about 5 years ago - Stars: 83 - Forks: 8

klebgenomics/Kleborate-viz

Visualisation application for Klebsiella genotypes generated by Kleborate.

Language: R - Size: 4.8 MB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 8 - Forks: 2

liviuspenter/ONT-lineage-tracing

Analyses of Penter, Borji & Nagler et al., 2023

Language: R - Size: 60.4 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

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: 30 days ago - Pushed: 4 months ago - Stars: 9 - Forks: 5

tseemann/nullarbor

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

Language: Perl - Size: 11.3 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 123 - Forks: 35

medvedevgroup/vargeno

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

Language: C++ - Size: 35.4 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 19 - Forks: 4

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: 7 months ago - Pushed: 7 months ago - Stars: 3 - Forks: 0

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

emm Automatic Isolate Labeller

Language: Jupyter Notebook - Size: 1.34 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 2

PengJia6/MSHunter 📦

Microsatellite genotyping

Language: Python - Size: 114 MB - Last synced: 8 months ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

casanova-lab/GMUSCLE

Genotyping MUltiplexed-Sequencing of CRISPR-Localized Editing

Language: Python - Size: 25.7 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 2 - Forks: 1

mohamed-malk/Z-care

Graduation Project (2023)

Size: 1.46 GB - Last synced: 5 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

bedapub/HBVouroboros

HBVouroboros automates sequencing-based HBV genotyping and expression profiling

Language: Python - Size: 23.5 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 2 - Forks: 1

ChaissonLab/danbing-tk

Toolkit for VNTR genotyping and repeat-pan genome graph construction

Language: Python - Size: 55.1 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 18 - Forks: 3

teepean/BAM-Analysis-Kit

Language: Forth - Size: 2.18 GB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 18 - Forks: 6

dbespiatykh/tblg

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

Language: Python - Size: 40 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

transbioZI/Gimpute

An efficient genetic data imputation pipeline

Language: R - Size: 2.93 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 10 - Forks: 4

ahryho/psychoGE

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

Language: HTML - Size: 315 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

AlgoLab/MALVIRUS

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

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

ut-biomet/breedSimulatR

R 📦 providing classes and functions to simulate breeding schemes.

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

akikuno/DAJIN

One-step genotyping software using a long-read sequencer

Language: Python - Size: 36.3 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 2

stjude/indelPost

Python library for simple and complex indels.

Language: C - Size: 1.17 MB - Last synced: 28 days ago - Pushed: 4 months ago - Stars: 11 - Forks: 3

phylo42/sherpas

Screening Historical Events of Recombination in a Phylogeny via Ancestral Sequences

Language: C++ - Size: 26.1 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 7 - Forks: 3

clemgoub/TypeTE

Genotyping of segregating mobile elements insertions

Language: Perl - Size: 62.5 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 18 - Forks: 1

datngu/SNP_array_comparison

Running codes and data analysis scripts for SNP array comparison paper

Language: Shell - Size: 1.23 GB - Last synced: about 1 year ago - Pushed: over 1 year 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: 20 days ago - Pushed: almost 2 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: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

gokalpcelik/ROHMMCLI

ROHMMCLI - Flexible HMM based homozygosity predictor.

Language: Java - Size: 272 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

germinateplatform/germinate-training

Training material for the use of Germinate

Language: SCSS - Size: 20.5 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

aryarm/VarBench

Benchmarking variant callers for long read data

Language: Python - Size: 105 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

czbiohub/sunbeam_gt-pro

Functional testing for gt-pro for microbial genotyping

Language: Python - Size: 82 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - 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: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

tseemann/amplikate

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

Language: Perl - Size: 129 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 1

pongorlorinc/mcaller

Language: Python - Size: 44.9 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0