16S rRNA Profiling - cloudfront.net

GenomInsight cloud starter package

16S rRNA Profiling* Your Need Bacterial microbiome profiling through 16S rRNA analysis and optional fungal profiling through ITS analysis, has become affordable and feasible from a data generation standpoint, with the arrival of benchtop next generation sequencing instruments. However, given the emerging nature of microbiota analysis as a scientific discipline and medical practice, downstream analysis is not as accessible in many situations as the upstream data generation.

16S rRNA profiling starter package contents project consulting

3 hrs

primary analysis

up to 64 sample x marker gene combinations

application configuration download of deliverables

biom & phyloseq format unlimited number of reports

permanent on-demand access†

3 months

data archival†

3 years

GI cloud

3 accounts 1 free e-Learning course of choice

Our Solution GeneCreek through its GenomInsight cloud bioinformatics platform, offers nonbioinformaticians the possibility to conduct exploratory microbiome data mining and report generation autonomously. Pre-processed data is hosted in a secure cloud environment and permanently accessible through a dedicated exploratory analysis web browser application.

a number of GI cloud accounts. Primary analysis results, tables and graphics can be downloaded for use in other applications and report. All graphics are obtained in publication quality vector line art format. The platform is entirely compatible with mobile browsers.

GeneCreek implements best practice translational microbiome data analysis using QIIME and various R Bioconductor packages, incorporating

GeneCreek provides e-Learning courses to promote best practices in microbiome analysis. To encourage self-paced learning, one e-Learning course of choice is included in the starter package. The courses contain exercise modules which make use of the same analysis modules as the analysis application, thus lowering the threshold for new users.

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open and closed reference OTU picking rarefaction alpha diversity analysis beta diversity analysis differential analysis - case/control & time series

Jump start microbiome profiling GeneCreek offers a 16S rRNA and ITS marker gene profiling starter package to new Customers. The package features consulting and application configuration services, unlimited access to the profiling application during a period of time and © GeneCreek 2016, all rights reserved

e-Learning

Requirements GeneCreek can work with Illumina fastq and Roche sff file formats as input data for analysis. GeneCreek can help with sequencing provider selection and partners with 3rd parties to ensure end-to-end implementation of best analysis practice. GeneCreek SAS - 196 rue du Rocher de Lorzier - 38346 Moirans - France GeneCreek Inc. - Trolley Square - Suite 20C - Wilmington - DE 19801 - USA

Experiment metadata can be accepted in various text file formats. Patient identities must be under no circumstances be communicated, all sample identifiers must be anonymized prior to start of service.

Recommendations Metagenome composition is highly specific to individuals and can exhibit variation over time, even without variation of conditions. It is recommended to use 6 or more biological repeats per time point and condition. Overcharging the number of conditions with respect to the total number of samples will lead to statistically under-powered studies. For many plots, limited display space is available for sample identifiers. Please consider using

acronyms for the identification of samples and leading zeros for numbers to achieve fixed width identifiers, e.g. C22D09

control individual 22, day 09

T02D12

case (treatment) individual 2, day 12

A1CD07

Assay 1 control group, day 07

Likewise, categorical metadata representation in results benefits from concise, fixed width acronyms.

Routine analysis GeneCreek is committed to making routine analysis from raw data to actionable results entirely possible for end-users. The self-service platform is expected to launch in spring 2017. Until then, flat fee-for-service analysis is proposed to Customers who have used the starter package and wish to engage routine, large-scale analysis.

T1AD07 T1CD07

Control

Treatment T1AD35

T1AD21

T1CD21

T1CD35

Fitness for use GeneCreek fully recognizes one-fits-all solutions for emerging application fields such as microbiome analysis are hard if at all possible to achieve. Which is why we are building the GenomInsight cloud platform - a flexible framework allowing for quick and reliable integration of new analysis modules.

GeneCreek

For Research Use Only. Not for use in diagnostic procedures. †GeneCreek uses Amazon Web Services (AWS) and disclaimers pertaining to AWS cloud availability and security apply to GeneCreek’s cloud services. For further information, please consult https://aws.amazon.com/s3/sla/, http://aws.amazon.com/security/ and https://www.genecreek.com/en/privacy-security/ *

NGS workflow and analysis

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