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Sequencing Platform of the Institut Pasteur

The Pasteur Genopole is organised around 5 platforms which are engaged in the production and analysis of high-throughput sequencing data : Genomics, Transcriptomics and Epigenomics, Genotyping of Pathogens and Public Health, Genotyping of Eukaryotes, and Genomic Bioanalysis. It offers a vast array of high throughput sequencing technologies : resequencing, de novo sequencing, targeted sequencing, identification of structural variants, identification and characterisation of new infectious agents, transcriptome and epigenomics analysis (ChIP-Seq). Through interactions with the Informatics Centre for Biology at the Institut Pasteur, it also contributes to the development of analysis pipelines and data analysis.

Equipment :
Sequencer : HiSeq2000
Bioruptor

Main achievements :
Genopole Pasteur conducts more than 80 projects annually. Microbiology and infectious diseases constitute its major areas of activity, but the platform also conducts projects on various topics related to human health (developmental biology, cancer) and model systems (yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe).

Bioinformatics analysis :
The sequencing platform of the Institut Pasteur offers the following services :

1. Genomic sequencing
Primary analysis
 Delivery of raw sequence data and quality scores
 Sequencing and quality control report
 Test for contamination
 Data filtering and cleaning
 Alignment of reads against a reference sequence
Secondary analysis
 DNA : de novo assembly
 DNA : Reference assembly
 DNA : Identification of SNPs
 DNA : Identification of indels

2. Whole Exome Sequencing
Primary analysis
Delivery of raw sequence data and quality scores
 Sequencing and quality control report
 Data filtering and cleaning
 Alignment of reads against a reference sequence
Secondary analysis
 Whole Exome sequencing
 DNA : Identification of SNPs and indels, Annotation.

3. RNA-Seq
Primary analysis
 Delivery of primary sequence data and quality scores
 Data pre-processing : adapter trimming, removal of low quality reads ...
 Mapping to a reference genome
 Quality estimation (percentage of reads that align to the genome, ribosomal contamination ...)
 Automatic printout of primary analysis reports (PDF files)
Secondary analysis
 Standardisation
 Differential analysis (establishing lists of differentially expressed genes)
 Automatic printout of statistical analysis reports (PDF files)
 Enrichment calculation (ontology and functional categories)

4. ChiP-Seq and MedIP-Seq
Primary analysis
 Delivery of primary sequence data and quality scores
 Data pre-processing : adapter trimming, removal of low quality reads ...
 Mapping to a reference genome
 Quality estimation (percentage of reads that align to the genome …)
Secondary analysis
 Standardisation
 Differential analysis, enrichment calculation.

Quality Assurance / Certification :
in progress

For further information : http://www.pasteur.fr/genopole

Platform Manager : Philippe Glaser

Genopole - Institut Pasteur
28 Rue du Dr Roux,
75724 Paris Cedex

Contact genopole@pasteur.fr


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