• Primary run analysis and quality control
  • Alignment of sequencing reads to the reference sequence using proprietary GEM alignment pipeline
  • Variant calling pipeline (SNVs and indels) including SamTools, GATK, Pindel and SNAPE
  • Proprietary variant filtering and prioritization tool
  • Identification of copy number variants (CNVs) with Control Free-C
  • Proprietary genome assembly pipeline using shotgun genome sequencing and/or fosmid pool approaches
  • Proprietary genome annotation pipeline for coding and non-coding RNAs
  • Differential expression analysis pipeline including proprietary GEM-split-mapper and Flux Capacitor for gene and isoform quantification
  • Identification of gene fusions from transcriptome reads
  • Cytosine methylation analysis pipeline including proprietary GEM mapper and bs_call
  • Determination of the higher-order chromatin folding of genomic domains and whole genomes using proprietary TADbit software
  • Storage and distribution of data in collaboration with the Barcelona Supercomputing Center (BSC)