ServicesBlocks

OVERVIEW

The CRG Bioinformatics Core facility provides researchers at CRG-CNAG/PRBB and external organizations, both academic and commercial, with services of consultation, planning Next Generation Sequencing (NGS) and other genomic experiments, data processing, analysis and management, software and database development, bioinformatics training, and access to high-performance computing resources at CRG.

BioCore works in synergy with the other CRG core facilities, including Genomics Unit and Biomolecular Screening & Protein Technologies Unit, to support researchers throughout all steps of high-throughput experiments, from an experiment planning to delivery of timely and reliable results.

In addition to services provided for fee, we support fully collaborative grant-funded investigations. This includes preliminary data analysis, planning the grant budget and experiments provided by the CRG Genomics Unit, writing relevant sections of the proposal, data analysis and biological inference, custom software development, and co-authored dissemination of the grant results.

PROCEDURE

To request a service, a free consultation or to propose a collaborative project or a grant proposal, please contact us via email or phone.

We encourage researchers to discuss both experimental and bioinformatics procedures before submitting materials for sequencing at the CRG Genomics Unit. We can help with advising on different options and minimizing costs.

After an agreement on the provided services and deliverables is reached, before starting working, we issue an official quotation, which has to be approved by the user in writing (via e-mail). By agreeing with the quotation, the user enters into the contract with CRG and agrees with our Terms and Conditions of the service.

Our turnaround time for completing the service is 3-10 business days, depending on the request’s complexity and the current capacity. For standard requests (read pre-processing and QC, read mapping, mRNA-seq, miRNA-seq, ChIP-seq, 16S rRNA, microarray, WES variant calling), we can usually provide an accurate estimate of delivery time, at the time of the initial meeting.

Throughout the project, we carefully document our work and constantly communicate with the researchers on the progress and revise initial goals if needed. To avoid unnecessary expenses, if the problem with the data quality was spotted, we communicate it right away.

When the request is completed, we issue an invoice on actual accounted hours (please refer to the page FEES below). We can also provide the final written report, facilitate preparation of relevant sections of publications, and handle submission of data to public repositories. The original and derived data are guaranteed to be stored at CRG for 6 months after completion of the request.

FEES

All our communication with users, including consultations, meetings, quotations, and e-mail/skype communication, is free of charge.

Please refer to the cost estimates for standard bioinformatics services and to the CRG webpage for our current fees for manual (Data Analysis, Database Maintenance Support, Programming / Database Development) and computing hours (Automatic Data Analysis) for CRG/PRBB and other public organizations. Prices for commercial users are subject of negotiation.

GENOMICS

De novo and reference-based assembly of eukaryotic and prokaryotic genomes.
Genome re-sequencing and quality assessment of genome assemblies.
Whole exome and whole genome analysis: variant calling, CNVs.
Identification and annotation of DNA structural variants for common and rare human diseases: individual and family analysis, cancer driver gene mutations.
Genomes comparison.
Genome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, and other DNA regulatory elements.
Analysis of 5C, Hi-C and other high-throughput data.

TRANSCRIPTOMICS

De novo and reference-based assembly of eukaryotic and prokaryotic transcriptomes.
Transcriptome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, and other regulatory elements.
Variant calling from transcriptome sequencing data.
Analysis of commercial and custom microarrays: differentially expressed genes, group comparison.
RNA-seq for mRNA: discovery of new transcripts, differentially expressed genes/transcripts.
Functional analysis of differentially expressed genes/transcripts: Gene Ontology terms, DNA motifs, and pathways enrichment analysis.
RNA-seq for small and non-coding RNA: differential expression, discovery of new microRNAs, microRNA target prediction.
ChIP-seq (TFs, histone modifications): peak calling, differential binding analysis among sample groups, peak annotation.
Analysis of ATAC-seq, OpenArray real-time PCR, and other high-throughput experimental data.
Identification of batch effects and visualization of data and results: hierarchical clustering, heatmaps, dendrograms, volcano plots, principal components analysis for the overall (dis)similarity among experiments.
RNA-target-based sequencing: RIP-seq, iCLIP, CLIP-seq, and other.

METAGENOMICS

Analysis of amplicon (16S/18S rRNA genes) and whole genome and transcriptome shotgun sequencing data:
Identification of microbial communities, taxonomic diversity and abundance at the sub-species levels (genus, family, order, class, phylum).
Conservation and abundance of bacterial gene functional modules and biochemical pathways.
Estimation of microbial diversity and sequence coverage.
ORF prediction and functional annotation.
Generating phylogenetic trees.
Comparative analysis of samples: microbial profiles, Gene Ontology terms, metabolic and pathway analyses.

PROTEOMICS & STRUCTURAL BIOINFORMATICS

Protein functional annotation and prediction.
Analysis of SNPs and other variations effects on protein structure and function.
Multiple sequence alignment.
Orthologs and paralogs assignment.
Phylogenetic analysis and tree construction.
Protein structure comparison and 3D homology modeling.
Protein-protein and protein-ligand 3D docking.
B- and T-cell epitope prediction.