The vast majority of modern genomics protocols yield data which require fundamental bioinformatics analysis accompanying the final deliveries. The Genomics Facility offers the required bioinformatics support at various levels, spanning basic bioinformatics processing spanning basic quality control and alignment to reference genomes as well as basic statistical analysis for most projects, up to more advanced bioinformatics analytics based on collaboration agreements. Furthermore, the Genomics Facility is staffed and supported by the Fleming Computational Biology and Bioinformatics groups, ensuring the highest possible quality of specialized services and the application of the most up-to-date computational pipelines and bioinformatics protocols.
Basic Bioinformatics services include:
- Standard quality control at the raw short read level
- Alignment to the reference genome, customized according to the underlying protocol
- Basic differential expression analysis for RNA-Seq experiments using metaseqR2 (see also below)
- Basic data visualization (UCSC Genome Browser tracks)
Depending on the applied protocol and the analysis depth requested by the collaborator, the Genomics Facility is applying state-of-the-art, published and widely accepted tools developed by Fleming Bioinformaticians and Bioinformatics researchers. More specifically:
- For RNA-Seq protocols, further quality control and differential expression is performed with the metaseqR2 Bioconductor package developed by Fleming researchers. metaseqR2 successfully combines multiple analysis algorithms contributing to final accuracy while at the same time produces fully interactive reports and visualizations at various data layers. Full report examples can be found here, here and here.
- Moreover, for RNA-Seq protocols, additional interactive RNA-Seq data analytics and live analyses are available through the SeqCVIBE platform developed by Fleming researchers, upon additional collaboration agreements. A demo instance of the platform hosting pubic data and supported by ELIXIR-GREECE can be found here.
- For ChIP-Seq and related protocols (e.g., ATAC-Seq), apart from standard peak calling with algorithms such as MACS and PeakRanger, advanced signal visualizations are available through the Bioconductor package recoup also developed by Fleming researchers.
- For metagenomics protocols (e.g., 16S sequencing), the Ion Proton optimized metagen pipeline is applied, producing comprehensive reports of the results.
- For genomics protocols including DNA variant calling at whole exome or genome level, a protocol developed by Fleming researchers including three modern variant callers and basic variant annotation is applied.
Apart from advanced bioinformatics services which are standardized, additional advanced services such as clustering, functional enrichment, pathway analyses, variant annotation etc., or custom analyses for specialized protocols are available upon requests and collaboration agreements.