Genepi Innsbruck
This site summarizes our main software projects. The focus of our projects is on mitochondrial DNA (mtDNA), Genotype Imputation, genome wide association studies (GWAS) and general frameworks for big data analysis.
For a list of all projects click here or visit the website of our institute.
mtDNA
| Project | About | Reference | Publication |
|---|---|---|---|
| Haplogrep | HaploGrep is a tool for mtDNA haplogroup classification. | https://github.com/seppinho/haplogrep-cmd https://haplogrep.i-med.ac.at/ | Human Mutation 2010 Nucleic Acids Research 2016 |
| Haplocheck | Haplocheck detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content. | https://github.com/genepi/haplocheck https://mitoverse.i-med.ac.at/ | Genome Research 2021 |
| mutserve | Mutserve is a variant caller for the mitochondrial genome to detect homoplasmic and heteroplasmic sites in sequence data. | https://github.com/seppinho/mutserve https://mitoverse.i-med.ac.at/ | Nucleic Acids Research 2016 |
Please contact Sebastian or Hansi in case of questions.
Imputation
| Project | About | Reference | Publication |
|---|---|---|---|
| Michigan Imputation Server | Michigan Imputation Server provides a free genotype imputation service using Minimac4. | https://github.com/genepi/imputationserver https://imputationserver.sph.umich.edu | Nature Genetics 2016 |
| Imputationbot | Automate interactions with Michigan Imputation Servers. | https://github.com/lukfor/imputationbot |
Please contact Lukas or Sebastian in case of questions.
GWAS
| Project | About | Reference | Publication |
|---|---|---|---|
| PGS Calculation | Applying polygenic scores (PGS) on imputed genotypes. | https://github.com/lukfor/pgs-calc | |
| nf-gwas | A nextflow pipeline to perform genome-wide association studies using regenie. | https://github.com/genepi/nf-gwas |
Please contact Sebastian or Lukas in case of questions.
Frameworks
| Project | About | Reference | Publication |
|---|---|---|---|
| Cloudgene | A framework to build Software As A Service (SaaS) platforms for data analysis pipelines. | https://github.com/genepi/cloudgene | BMC Bioinformatics |
| Cloudflow | Simplified pipeline creation for MapReduce and Spark. | https://github.com/genepi/cloudflow | IEEE Conference 2015 |
| genepi-libs | This repository includes libraries which are used in many of our scientific projects. | https://github.com/genepi/genepi-libs |
Please contact Lukas or Sebastian in case of questions.
Teaching
| Project | About | Reference | Publication |
|---|---|---|---|
| NGS-Class | Introduction to bioinformatic analysis of next (NGS) and 3rd generation sequencing data. | https://github.com/genepi/ngs-class |