RADseq Data Exploration, Manipulation and Visualization using R

Support Vector Structural Variation Genotyper

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

stackr: an R package to run stacks software pipeline

Population assignment analysis using R

A collection of WDL bioinformatic workflows to benchmark markers coming from different pipelines using linkage map quality as a diagnosis.

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

A clinical decision-support system to identify pharmacogenomics profiles based on subjects genotype of five core genes. The paper has been published in the Journal of Personalized Medicine.

An advanced genotyping pipeline by next-generation sequencing (NGS) technology

StaphScope is a comprehensive bioinformatics tool for Staphylococcus aureus genomic analysis including MLST typing, spa typing, SCCmec analysis, antimicrobial resistance detection, virulence factors, plasmid profiling, and lineage prediction from whole genome sequencing data. Designed specifically for MRSA research

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

🕊 This repository is associated with the manuscript Pacheco et al. (2020).

pipeline to perform gbs and genetic fitness analysis

Germline SNV calling and phasing from single cell sequencing (for macOS Sequoia and Rocky8).

Tutorial for Genotyping by RNA Sequencing (GBRS), which quantifies transcripts via RNASeq and genotypes the samples using SNPs in transcripts.

Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)

CODEHOP-mediated genotyping of HIV-1

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 and GBS statistics generation

Repo containing all scripts associated with Mahoenui giant wētā population genomic analysis from GBS data