The philosophy behind Cloudgene is to hide complex MapReduce processes from end users.
What is Cloudgene?
Cloudgene is a freely available platform to improve the usability of MapReduce programs by providing a graphical user interface for the execution, the import and export of data and the reproducibility of workflows on in-house (private clouds) and rented clusters (public clouds).
The aim of Cloudgene is to build a standardized graphical execution environment for currently available and future MapReduce programs, which can all be integrated by using its plug-in interface.
Who uses Cloudgene?
Cloudgene lives from its applications. Therefore, we already integrated available MapReduce programs in the field of genomics such as HadoopBam, Seal, Crossbow, Cloudburst, Myrna into Cloudgene. If you’re interested to integrate your program and need help with the set-up, please let us know.
Imputationserver (University of Michigan)
This server provides a free genotype imputation service. You can upload GWAS genotypes and receive imputed genomes in return. The underlying imputation engine is base on minimac, which implements a low memory, computationally efficient algorithm for genotype imputation that can handle very large reference panels with thousands of haplotypes. The current version of this server uses the 1000 Genomes Project phase I release as a reference for imputation.
mtDNA-Server (University of Innsbruck)
This server provides a free mtDNA alignment and heteroplasmy detection service. You can upload either single/paired FASTQ or BAM files and receive BAM files (in case of FASTQ input), detected heteroplasmies, interactive reports and haplogroups in return. The current version of this service uses a parallelized version of BWA MEM for alignment and includes different filters (e.g. BAQ, quality filters, statistics methods) to determine heteroplasmies reliable. All steps are executed in parallel using Cloudgene and the Hadoop framework.