Services

FOCUS

The Bioinformatics Unit supports researchers at CRG, PRBB, and beyond with high-throughput sequencing data analysis, experimental planning, and bioinformatics solutions that foster reproducible research, as well as training to disseminate good practices. We work in synergy with other CRG Core Technologies units.

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 Centre for Genomic Regulation (CRG) for assistance with <services performed>.” Please refer to the CRG Core Technologies Terms and Conditions.|

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 Centre for Genomic Regulation (CRG) for assistance with <services performed>.” Please refer to the CRG Core Technologies Terms and Conditions.

(EPI)GENOMICS

WGS and WES: variant calling, CNVs
Long-read DNA-seq (ONT, PacBio Revio): assembly, methylation, SVs
ChIP-seq (TFs, histone modifications): peak calling, differential binding analysis among sample groups, peak annotation
ATAC-seq, CUT&RUN
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, and other DNA regulatory elements

(EPI)TRANSCRIPTOMICS

ONT dRNA-seq: RNA modifications, A-tail length, isoforms identification
Single-cell RNA-seq, short and long reads
RNA-seq for mRNA: differentially expressed genes/transcripts, discovery of new transcripts
RNA-seq for small and non-coding RNA: differential expression, discovery of new microRNAs, microRNA target prediction
Functional analysis of differentially expressed genes/transcripts: Gene Ontology terms, DNA motifs, and pathways enrichment analysis
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 T cell repertoires (adaptive immune receptor repertoires, or AIRR) from high-throughput sequencing data: germline allele assignment, identification of clones, visualization of clonal frequencies

METAGENOMICS

Analysis of amplicon (16S rRNA genes / ITS), whole genome and transcriptome shotgun sequencing data (short and long reads)
Identification of microbial communities, taxonomic diversity and abundances at the levels of genus, family, order, class, phylum
Conservation and abundance of bacterial gene functional modules and biochemical pathways
Estimation of microbial diversity and sequence coverage

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
Linux containers: development, testing, deployment (HPC, Cloud), maintenance|

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
Linux containers: development, testing, deployment (HPC, Cloud), maintenance

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:

Support Cloud (AWS) computing (we maintain the AWS infrastructure for online hands-on training)
Statistical analysis and plots: R scripts, descriptive and inferred 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
Data submission to GEO, ArrayExpress, SRA, and other public data repositories
Mining public databases and publications and re-analyzing published data
Manuscript preparation: writing methods, results, 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|

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:

Support Cloud (AWS) computing (we maintain the AWS infrastructure for online hands-on training)
Statistical analysis and plots: R scripts, descriptive and inferred 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
Data submission to GEO, ArrayExpress, SRA, and other public data repositories
Mining public databases and publications and re-analyzing published data
Manuscript preparation: writing methods, results, 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