COGEDAP: A COmprehensive GEnomic Data Analysis Platform
Non-sharable sensitive data collection and analysis in large-scale consortia for genomic research is complicated. Time consuming issues in installing software arise due to different operating systems, software dependencies and running the software. Therefore, easier, more standardized, automated protocols and platforms can be a solution to overcome these issues. We have developed one such solution for genomic data analysis using software container technologies. The platform, COGEDAP, consists of different software tools placed into Singularity containers with corresponding pipelines and instructions on how to perform genome-wide association studies (GWAS) and other genomic data analysis via corresponding tools. Using a provided helper script written in Python, users can obtain auto-generated scripts to conduct the desired analysis both on high-performance computing (HPC) systems and on personal computers. The analyses can be done by running these auto-generated scripts with the software containers. The helper script also performs minor re-formatting of the input/output data, so that the end user can work with a unified file format regardless of which genetic software is used for the analysis. COGEDAP is actively being used by users from different countries/projects to conduct their genomic data analyses. Thanks to this platform, users can easily run GWAS and other genomic analyses without spending much effort on software installation, data formats, and other technical requirements.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
Functional Integrative Bayesian Analysis of High-dimensional Multiplatform Genomic Data
Rapid advancements in collection and dissemination of multi-platform molecular and genomics data has resulted in enormous opportunities to aggregate such data in order to understand, prevent, and treat human diseases. Wh…
Data IntegrationPrognosisVariable SelectionVocal Bursts Intensity PredictionGuide to k-mer approaches for genomics across the tree of life
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. H…
DiversityData Lakes, Clouds and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharin…
Cloud ComputingManagementFAPS: A Fast Platform for Protein Structureomics Analysis
Protein quantification and analysis are well-accepted approaches for biomarker discovery but are limited to identification without structural information. High-throughput omics data (i.e., genomics, transcriptomics, and …
Just-DNA-Seq, open-source personal genomics platform: longevity science for everyone
Genomic data has become increasingly accessible to the general public with the advent of companies offering whole genome sequencing at a relatively low cost. However, their reports are not verifiable due to a lack of cru…