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The Bioinformatics Surveillance Platform

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AlignDx is a web-first platform for running automated bioinformatic workflows for pathogen detection/surveillance. The core of the platform is a dynamic workflow system, that generates pipelines and their respective web-forms based on a collection of schemas. Supporting this is authentication, archiving and task queueing, to deliver a seamless experience.

In the sequencing-based workflow, the user uploads one or more sequencing datasets (.fastq files) and AlignDx screens each dataset for the presence of pathogens based on a user-selected "pathogen panel" (e.g., human pathogenic viruses). AlignDx then runs Kraken2 and Bracken on each .fastq file and outputs the: estimated abundance of pathogens in the full dataset, and the estimated abundance of pathogens in the full dataset excluding human reads.

The raw data uploaded by users are removed following analysis, but the analysis results are archived for later viewing and associated only with a specific user account to facilitate data privacy. In addition, additional data for each run can be downloaded for offline viewing such as the full set of taxonomic predictions and associated files generated by Kraken2 and Bracken.

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1. Install docker and docker compose.
2. Install git if you don't have it already.

1. Clone the repo

   git clone https://github.com/doxeylab/aligndx.git

2. Setup the project environmental variables in an .env file, located in the root directory. For details, see this section.

3. Install the app using the build script. Scripts are provided for both production and local usage respectively.

   ./build.sh 

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1. Users can register on the platform by accessing the appropriate URL (as setup in the environment file)

2. The following is a diagram outlining the typical workflow a user might follow using the platform UI.

   

   Stepwise utilization of Lookout in the AlignDx Platform. (A) Workflow/pipeline selection menu and (B) available workflow options. (C) Surveillance specific form components. (D) Filled out surveillance form, with input dataset, and chosen options. (E) Status card for monitoring submissions. (F) Workflow output report. (G) Archive entry for submission.

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Distributed under the GPLv3 License. See License.txt for more information.

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Manjot Hunjan - [email protected]

Project Link: https://github.com/doxeylab/aligndx

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Thanks to our many collaborators!

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