ATGC: NGS - Next Generation Sequencing

Next Generation Sequencing (NGS)

Computational services

The HTS platform provides services for analyzing HTS sequencing data with respect to a reference sequence (usually a reference genome or an assembled transcriptome). The services goes from a single step in a pipeline to a complete analysis taking reads as input and yielding predictions of various kinds (splicing junctions, expressed genes, mutations, potential chimeric RNAs). For a complete analysis, most steps (e.g. mapping) exploit the read and the genome sequences, while the latter cross the predictions with genomic annotations if available. The proposed analysis depends on the type of HTS data: whether these come from genomic sequencing, a RNA-seq or a Digital Gene Expression assay, and on the sequencing platform.
We propose the following services on standard basis:

Mapping to a reference genome or an assembled transcriptome
Mapping background and error rate estimation
Identification of erroneous bases (in comparison to a reference genome)
Prediction of mutations: SNP, somatic mutations, small and medium size indels
Identification of spliced reads and of potential splicing junctions
Identification of potential chimeric RNAs
Annotation and classification of sequenced or transcribed regions (depend of annotations)

Mapping and some other services are also applicable to

Cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq)
Chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing (ChIP-seq)