Helixio, bioinformatics service provider
Genomic data from high-throughput technologies require know-how and skills in bioinformatics and data analysis to extract meaningful information.
Helixio is a service provider in genomics and bioinformatics: our experienced team will help you interpret your genomic data in an efficient and didactic way.
All data generated during your project are provided: quality control data, raw and standardized sequences, alignment files and detailed analysis report. Data is stored for 2 to 6 months depending on the technology used.
A project manager, assigned to your study, is available to discuss at each stage of the analysis, including after the final report has been submitted.
We use open-source bioinformatics tools, commercial applications and develop our internal pipelines: we use the strategy that best suits your data and your needs.
NGS data analysis
Different steps are necessary to extract the relevant information.
The primary analysis includes quality control, sequence trimming and adapters removal. After alignment on the reference genome, it is possible to identify variations and rearrangements of the genome. For organisms without a known and published reference, de novo assembly is appropriate.
Reads from RNA-seq data allow in particular the quantification of gene expression and the identification of differentially expressed transcripts according to a study parameter.
The steps listed above are part of the standard workflows applied to our NGS services.
Standard workflow for a DNA-seq study
RNA-seq standard workflow
Standard workflow for microbiome analysis
Custom analysis
Helixio offers standard and custom solutions. Our team can tailor their workflows to your needs and develop project-specific pipelines that meet your requirements and data. Whether or not they are generated by Helixio, we will help you interpret them in the most relevant way.
- Example of specific analyses:
De novo assembly and functional annotation of a poorly characterized eukaryotic organism in public databases
When an organism is rare or poorly documented in databases, its identification and characterization require a suitable bioinformatics strategy. In this context, an approach combining shotgun metagenomics and metatranscriptomics allows to reconstruct and annotate the genome and transcriptome of an unknown organism.
In a specific case of an unidentified eukaryotic organism, Helixio has developed an innovative bioinformatics tool:
- A first phase of analysis of shotgun metagenomic data made it possible to identify the species closest to the unknown organism, then to carry out a first de novo assembly despite a limited set of data.
- Subsequently, the reconstruction of the transcriptome from metatranscriptomic data has improved the quality of the assembly by relying on previously identified gene families of interest, as well as from our own combined databases.
Thus, this strategy has allowed the precise identification of the species, as well as a functional annotation to predict biological functions.
And you, do you work on complex samples or poorly characterized organisms? Do you have complex problems?
So, don’t hesitate to contact us!