1. Primary run analysis and quality control
  2. Alignment of sequencing reads to the reference sequence using proprietary GEM alignment pipeline
  3. Variant calling pipeline (SNVs and indels) including SamTools, GATK, Pindel and SNAPE
  4. Proprietary variant filtering and prioritization tool
  5. Identification of copy number variants (CNVs) with Control Free-C
  6. Proprietary genome assembly pipeline using shotgun genome sequencing and/or fosmid pool approaches
  7. Proprietary genome annotation pipeline for coding and non-coding RNAs
  8. Differential expression analysis pipeline including proprietary GEM-split-mapper and Flux Capacitor for gene and isoform quantification
  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)