
- Primary run analysis and quality control
- Alignment of sequencing reads
- Validated variant calling pipelines for SNVs, InDels, CNVs and Structural Variants
- Benchmarked pipelines for the identification of somatic mutations
- Variant filtering, prioritization and interpretation
- Proprietary genome assembly pipeline using shotgun genome sequencing and/or fosmid pool approaches
- Proprietary genome annotation pipeline for coding and non-coding RNAs
- Gene and isoform quantification using the ENCODE RNA-seq data processing pipeline (STAR+RSEM)
- 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)