
- 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)