Slovenski genomski projekt / Slovenian genome project (SGP)
Ta repozitorij je uradni repozitorij Slovenskega genomskega projekta. Vseboval bo izvorno kodo analitičnih poti, standardov in priporočil dobre prakse za analizo podatkov celotnega genoma, ki jih bomo opravili v sklopu 2. delovnega sklopa projekta (DS2).
This code repository is an official repository of the Slovenian genome project. It will contain the pipelines, accepted standards and guidelines for processing of whole genome sequencing data withing work package 2 (WP2).
Aims of the Data analysis group in SGP
This work package has several goals
- Select the state-of-the-art standards for genomic data storage and analysis of the Slovenian genome project sequencing data
- Implement the current best practice pipelines for WGS data generated during the project
- Enable connections and alignment with other genome sequencing initiatives (1M+ genomes initiative by the EU Commission)
- Develop a resource of variability in the Slovenian population
The contents
This repository is organized in the following main sections
- GATK_pipelines This folder contains the relevant code of the primary pipeline used for data processing, including the modifications and additions by WP2 team
- Standards This folder contains the information on the accepted formats, standards and guidelines for data processing
- Quality This folder contains code to perform QC of the data and to validate the analysis results against the accepted standards
- Projects This folder analysis projects contributed by the WP2 team
- Other Assorted files and documents