1. Primary run analysis and quality control
  2. Alignment of sequencing reads
  3. Validated variant calling pipelines for SNVs, InDels, CNVs and Structural Variants
  4. Benchmarked pipelines for the identification of somatic mutations
  5. Variant filtering, prioritization and interpretation
  6. Proprietary genome assembly pipeline using shotgun genome sequencing and/or fosmid pool approaches
  7. Genome annotation of coding and non-coding RNAs
  8. Gene and isoform quantification using the ENCODE RNA-seq data processing pipeline (STAR+RSEM)
  9. Identification of gene fusions from transcriptome reads
  10. Cytosine methylation analysis pipeline including proprietary GEM mapper and bs_call
  11. Determination of the higher-order chromatin folding of genomic domains and whole genomes using proprietary TADbit software
  12. Storage and distribution of data in collaboration with the Barcelona Supercomputing Center (BSC)