A pipeline specifically designed for the analyses of virology data. Using the Athena virology pipeline, you have access to the following features:
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DDL has a strong focus on virology and microbiome, therefore we have developed pipelines specific for the analyses of viral and microbiome NGS data. We can also tailor our existing pipelines to suite your special needs or develop a tailor made pipeline for you. See below for more information on our unique pipelines.
At DDL we work in multi disciplinary teams where we combine the knowledge of PHD grade scientists and senior bioInformaticians in order to create the optimal solution for our customers. With our scientific knowledge we are able to provide you a fully GxP compliant pipeline that has been scientifically validated.
We understand the importance of not only generating high quality data but also being able to deliver this data into your own clinical database or provide the output in submission ready formatting to FDA. We can assign a datamanager to your project who will ensure the quality, formatting (CDISC/SDTM) and compliancy of data for you. This makes DDL a unique partner.
Illumina v1.8 + Phred + 33 paired-end paired-end Fastq files are used on the pipeline.
Genotyping gives the percentage of reads that map to a specific reference. Raw reads from the fastq file are compared against all geno- and subtype reference sequences from a specific organism and mapping percentages are extracted. The sample is characterized with the highest percentage genotype.
Perform in-house programmed variant calling on a mapping of the data reads to determine the similarities and differences to the selected reference genome on genome level (nucleotide mapping) and on target level (amino acids, codons, single nucleotide variants).
An important step of the pipeline is to detect Sample swaps and contaminations that could occur during a sequencing run preparation, but more importantly, on the client’s side. For that reason we have developed a QC tool that can detect contaminations and output a QC report, ensuring there are no unpleasant surprises in downstream analyses.
Sample compositions of samples of different genotypes cannot be compared to each other due to inherent differences between genotypes. But the records can be converted from any reference to a universal one, so that they can be compared.
The record files can be exported in many formats, based on client requirements. The default are tab separated text files that are easy to import in Excel or an in-house database.
A pdf report can be generated automatically per Sample. This report contains sequencing quality data (fastq file QC and whole genome and per-target coverage graphs) and the genotyping results (if applicable).
A bacterial pipeline using next-generation sequencing data of the 16S region. The pipeline consists of the following features:
Illumina v1.8 + Phred + 33 paired-end Fastq files are used on the pipeline. Any 16S variable region that is sequenced can be used.
High quality input data is of utmost importance for detecting bacteria with Next-Generation Sequencing. Read quality trimming and denoising is performed to remove bad quality data from the dataset. For paired-end amplicon sequencing, forward and reverse reads are merged into one single sequence. Furthermore, chimera sequences (artificial sequences resulting from a-specific PCR reactions) are removed so that a clean dataset can be used for classification.
Good quality reads are used in classification analysis in order to identify which bacteria are present based on the 16S sequence. The sequencing reads are compared with a 16S database and each read is assigned to a taxonomy. Using the frequency of reads assigned to the same taxonomy, relative frequencies can be calculated and displayed in bar charts. These bar charts (per sample) can be compared with each other to gain insight in changes of the microbiome.
The relative frequencies resulting from classification analysis can be used in alpha and beta-diversity analysis. The alpha diversity analysis will generate results on the diversity within a sample, whereas beta-diversity analysis will measure diversity changes between samples. Various measures can be used for both analyses, with the most common ones being Shannon diversity for alpha-diversity analysis and PCOA analysis (3D scatter plot) for beta-diversity analysis.
Based on your requirements we can develop a custom pipeline for you
Projectmanagement
Every project has a dedicated projectmanager who ensures scope, planning and delivery of your pipeline. We use an agile project management method.
Pipeline design
Together with your own scientists we design the pipeline to fit your needs. This is where our scientists come in to assist you on the scope of the project and the specific needs for your type of analyses. We thoroughly describe requirements and will specify this in a statement of work.
Pipeline development
We develop the pipeline for you, this is a close collaboration between our bio informaticians and scientists. We have broad experience with open source tools and if needed we have the ability to develop a pipeline in Python for you. Our own Athena Virology pipeline is build in python and used by multiple top-20 pharma companies.
Pipeline hosting
After the pipeline has been created you want to make it available to your internal organization (or other stakeholders). DDL offers two options for that:
Pipeline validation
Perhaps one of the most challenging aspects of bioinformatics is the validation of the pipeline. At DDL we offer you completely validated and scientific validated pipelines. All software is fully auditable and reproducable. All our systems are GxP and 21CFR part 11 compliant to ensure record authenticity, integrity and confidentiality.
What does this mean?
Our technical implementation is fully documented. For this we follow a risk based approach based on the GAMP5 standard. This ensures that the software is fully documented and technically validated. You receive a extensive validation report.
Second there is the scientific validation. Every pipeline comes with one or multiple scientific validation reports where we prove that the analyses performed by the software is indeed scientifically correct. You receive a extensive scientific validation report.
GxP & FDA
From our background in assay development and clinical trial support we understand the importance of compliancy. All our pipelines are fully compliant to GxP requirements and are built following the guidelines of the FDA.
Datamanagement
We have a dedicated datamanagement department who can help you in setting up data transfer formats following CDISC standards and setup the output of the data in a compliant format.
BioCompute Object (Research project)
DDL participates in the FDA and George Washington University initiative of BCO in order to create a standard for the description of data analyses pipelines.
The Athena pipeline is the first virology pipeline that will be BCO described.
For more information please see https://biocomputeobject.org/
DDL works together with Seven Bridges in order to ensure a compliant and reliable platform for your analyses.
We can provide access to our Athena Virology pipeline via the Seven Bridges platform allowing you to run the pipeline on a high performance computing environment. With fully transparant and predictive costs and without any large investments in infrastructure or software.
We take care of the deployment of the pipeline on the environment. That way you can focus on the output and analyses of the data instead of worrying about virtual machines, processors and memory.
Just give us a call, send us an e-mail or make an appointment!
To learn more about our sister company Viroclinics
please visit: www.viroclinics.com
