At today, the Bioinformatics, Computational Analysis & Data Management unit (BAC) can support/collaborate with you in the following analyses:

Genomics:

  • Assembly & clustering
  • Genome composition assessment (GC/CpG etc content)
  • Conserved non-coding elements (CNE) prediction
  • Prokaryotic genome annotation (via Prokka)
  • Secondary metabolite prediction (via antiSMASH)

Transcriptomics:

  • Complete RNA-seq analysis with de novo assembly (from cleaning to DEGs calling)
  • Complete RNA-seq genome based analysis (from cleaning to DEGs calling)
  • Coexpression analysis (via WGCNA)
  • Gene Ontology enrichment analysis
  • ORF prediction (via TransDecoder)

Metagenomics/Metabarcoding:

  • Assembly & clustering
  • Prokaryotic genome binning
  • OTU/ASVs/sOTUs table analysis and statistical analysis of microbiome studies

GIS and Ecological modelling:

  • Data collection and/or integration using public/private data
  • Data mapping through GIS software/tools
  • Spatial analysis of environmental/biological data
  • Geoportal development and management
  • Ecological modelling (e.g. species distribution models and ecological niche models)
  • Support in data organization

Comparative analysis:

  • Orthology/paralogy prediction
  • Complete comparative analysis (networks of orthologs and paralogs)

Functional annotation:

  • Functional annotation (via BLAST vs. non reduntant database)
  • Functional annotation (via BLAST vs. UniprotKB or InterProScan)

Protein structure:

  • Three-dimensional protein structure prediction (via homology modeling)
  • Molecular dynamics simulations

Genomics platform setup:

  • Genome browser (JBrowse setup and population)
  • BLAST server setup

Systems configuration and tuning:

  • Linux server installation, configuration, tuning
  • Data storage systems setup
  • Software/full pipeline installation on single server

HPC computing and system design:

  • HPC compute node access (2 max jobs, 64cpu, 20 jobs queued)
  • HPC cluster setup

Virtualization/containering deployment:

  • Containering solutions (Docker, LXD, Singularity)
  • Basic kubernetes cluster deployment (qbetto + kubedm)
  • Full KVM system setup + instances

Database/software development:

  • Database design
  • API design and development
  • Software design and development

Additional services:

  • “Ad-hoc” file parsing
  • Submission of sequence data to public databases (e.g. NCBI Sequence Reads Archive)

For any support, contact us!!!