APPLICATIONS
Whole genome sequencingSequencing or re-sequencing of a complete genome starting from extracted genomic DNA (provided by the customer). Obtained reads can either be mapped on a reference annotated genome (choose ‘Resequencing’) or de novo assembled (choose ‘De novo’).
RNA sequencingSequencing of transcripts starting from extracted total RNA (provided by the customer) in order to get a gene expression study using classical RNA-seq or to get the localisations of Transcription Starting Sites (TSS) using differential RNA-seq.
Metagenomics (gene focused)Sequencing of universal gene markers (16S for bacteria, ITS for fungi, 18S for eukaryotic parasites and Cox2 for nematodes) after PCR amplification in order to determine microbiota composition in a sample.
Amplicon sequencingSequencing of a specific PCR product (provoded by the costumer) in order to dertermine sequence variation in a population. This approach can be performed on PCR product including Ion Torrent system sequencing adapters (Ion Amplicon Library Preparation-Fusion Method User Guide.pdf) (choose ‘With adaptator’) or not including these adaptators (choose ‘Without adaptators’).
ANALYSIS
Whole genome sequencingMapping onto reference genome: obtained reads will be mapped using specific mapper(s) to generate a Sequence Alignment Map (SAM) file (extension: .sam).
In-house Pipeline (Ch’toyo) analysis protocol using our recently developed pipeline. This analysis will generate full genome + plasmid(s) content as well as SNPs DIPs analysis by multi comparison with close sequenced strains (available for small genomes only: viruses, bacteria, parasites, yeasts).
Primo analysis (de novo assembly): assembling of obtained reads in contigs. Output will be a multi fasta file and associated statistical values.
Secondary analysis (de novo assembly): simple annotation of obtained contigs by homology search on availed annotated genomes (transfert annotation).
RNA sequencingGene expression: differential expression study determine after normalization, RPKM calculation and statistical analysis.
RNA mapping: determination of Transcription Starting Sites by transcripts enrichment calculation between exonuclease treated and non-treated samples.
Metagenomics (gene focused)
Pipeline (Ch’berdoulle) Determination of microbiota composition and proportion, scarce curves and association study using in-house pipeline.
Amplicon sequencingSNP/DIP detection: comparison of sequenced samples to a reference sample to determined variations: mutations and small insertions/deletions.
Rare mutation discovery: determination of rare event mutation in a cell population