Services

FOCUS

The Bioinformatics Unit supports researchers at CRG, PRBB, and beyond with experimental design, high-throughput sequencing data analysis, and scalable bioinformatics solutions that enable reproducible and FAIR research, supported by training and dissemination of best practices. We work in synergy with other CRG Core Technologies units.

WORKING WITH US

To request a service or a free consultation, to propose a collaborative project or a grant proposal, please contact us via email or phone or submit a request in Agendo. Please discuss both experimental and bioinformatics procedures before submitting samples for sequencing as we can help you in selecting the best and cost effective approach.

For our current fees, please refer to the CRG webpage. All our communication with users, including consultations, meetings, and e-mails, is free of charge.

Please note that payment of fees for services and authorship are not mutually exclusive. Each Core personnel who has participated in the work sufficiently enough to take public responsibility for appropriate portions of the content should be recognized as co-author; co-authorship should follow commonly-accepted scientific practice. The recovery of Core expenses through the recharge system does not exclude the possibility of authorship for Core personnel. Similarly, authorship does not substitute for payment of Core expenses for services rendered.

All work performed by the CRG Bioinformatics core should be acknowledged in scholarly publications, posters, and presentations by a direct statement in the acknowledgement section “The authors would like to thank the Bioinformatics Unit of the Core Technology Programme of the Centre for Genomic Regulation (CRG) for bioinformatics support and data analysis.”

Fo more information, please refer to the Terms and Conditions of the Core Technology Programme of the CRG.

(EPI)GENOMICS

• WGS and WES: variant calling and annotation, CNVs
• Long-read DNA-seq (ONT, PacBio Revio): assembly, methylation (5mC), SVs and tandem repeats
• CRISPR pooled screens: guide quantification, QC, differential analysis
• ChIP-seq (TFs, histone modifications): peak calling, differential binding analysis among sample groups, peak annotation
• ATAC-seq and CUT&RUN: peak calling, differential accessibility, motif enrichment
• Single-cell ATAC-seq and multiome (10X)
• Reference-based and de novo assembly of eukaryotic and prokaryotic genomes
• Genome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, etc.

(EPI)TRANSCRIPTOMICS

• ONT direct RNA-seq: RNA modifications, poly(A) tail length, isoform identification
• mRNA-seq: experimental design (multi-factor, interactions), batch correction, normalization and QC (replicate concordance), differentially expressed genes/transcripts, alternative splicing analysis, isoform-level quantification
• small and total RNA-seq: differential expression, discovery of new microRNAs, microRNA target prediction
• Single-cell RNA-seq (short reads, ONT)
• Spatial RNA-seq (STEREO-seq, Visium)
• Functional analysis of differentially expressed genes/transcripts: DNA motifs, GO and pathways enrichment analysis
• Transcriptome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, etc.
• Variant calling from transcriptome sequencing data
• Analysis of T cell repertoires (adaptive immune receptor repertoires, or AIRR)

METAGENOMICS

• Amplicon (16S rRNA genes / ITS) and Whole Metagenome Shotgun sequencing (short reads, ONT)
• QC, host read removal, contamination filtering
• Taxonomic profiling of microbial communities (composition and diversity)
• Comparative analysis: differential abundance, PERMANOVA / beta diversity
• Functional profiling of microbial communities (gene families and pathways)

DATABASES, WEBSITES & SOFTWARE

We have an extensive experience in design, development and support of following bioinformatics resources (browse our related projects here):

• Databases: Relational, NoSQL
• Websites for data submission, search, and analysis
• Web-tools: integrative bioinformatics web applications, customized genome browsers
• LIMSs (Laboratory Information Management System)
• Software: development, refactoring, benchmarking, deployment into production, maintenance
• Nextflow pipelines: development, testing, deployment (HPC, Cloud), maintenance
• Containers: development, testing, deployment (HPC, Cloud), maintenance

OTHER

Please contact us with any bioinformatics problem you may have, even if it does not fit to those listed in our services. Being part of several bioinformatics communities and alliances we may find the solution or experts in the field. Among custom and additional services we provide are the following:

• Experimental design consultation
• Cloud computing support (we maintain the AWS infrastructure for online hands-on training)
• Statistical analysis and plots: R scripts, descriptive and inferential statistics, hypothesis testing, sample size estimation, PCA, clustering, linear regression, correlation, ANOVA
• Statistical modeling (e.g., for biomarker discovery, patient stratification)
• One-to-one training
• Hands-on training courses in Linux, git/GitLab/GitHub, FAIR and reproducible data analysis, and various bioinformatics topics
• Data submission to GEO, ArrayExpress, SRA, and other public repositories
• FAIR data and metadata support
• Mining public databases and publications and re-analyzing published data
• Manuscript preparation: writing methods, results interpretation and visualization
• Grant support: writing methods, methodology for data management and sharing, experimental and bioinformatics analysis design, obtaining preliminary results, and result interpretation