The bioinformatics platform
This TWB platform operates in the context of the sequence data analysis
of TWB's R&D projects.
The service offer of the TWB bioinformatics platform includes the de novo assembly of micro-organisms, re-sequencing and analysis of genomic variants and the differential expression analysis of genomes from RNAseq. TWB is also involved in metagenomics in order to identify certain enzymatic functions. The data can be supplied by public databases or from sequencing services.
TWB relies on local sequencing platforms and enjoys a privileged environment in terms of second and third generation NGS (“Next Generation Sequencing”) technologies. Indeed, the GeT network of platforms (genome and transcriptome
http://get.genotoul.fr/index.php?id=216&L=0&tx_ttnews[backPid]=18&tx_ttnews[tt_news]=225), possesses:
- second generation sequencers:
- Illumina HiSeq 2500 and 3000, MiSeq: “paired end” sequencing (sequencing of the two extremities of the fragments) with sizes ranging up to 300Pb
- Ion S5: up to 40 kb
- third generation sequencers: PacBio RSII and MinION, producing long sequences.
These platforms are in constant evolution, acquiring the latest technologies from year to year. They thus provide access to extensive local expertise and a network, in addition to access to all of the most advanced technical solutions for sequencing projects.
[bloc_note]Legend: The ION S5 sequencer generates small chips with only 4 million sequences, thus allowing more flexible multiplex sequencing of isolated micro-organisms or 40 kb fosmids.[/bloc_note] Concerning bioinformatic analyses,
the platform uses the local infrastructure of Bioinfo GenoToul for the power of calculation and disk space(
http://bioinfo.genotoul.fr/). This infrastructure also regularly develops this material, thus providing a comfortable bioinformatics working environment.
TWB is also committed to training usersin bioinformatic analysis in collaboration with SIGENAE (Information system of genomes and breeding animals) and the Bioinfo GenoToul platform, with the Galaxy software tool (
http://bioinfo.genotoul.fr/index.php?id=10). The local Galaxy entity allows the integration of customised tools (
https://galaxyproject.org/) and user-friendliness. [bloc_enavant]
TWB offers a complete packagefrom the outset of the project for matching the different interlocutors (sequencing, bioinformatics analysis, biostatistics, training, etc.) and enables the partners to quickly obtain information in response to their questions.[/bloc_enavant]
Examples of applications
- Sequencing of strains of fungi, assemblage and annotation of genomes
- Analysis of the differential expression of the genes of 2 samples from 2 different conditions of culture of a plant
- Phylogenetic analysis of protein families (micro-organisms, plants) Training in Galaxy software
