classicvalues / bmgap

The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples

Bacterial Meningitis Genome Analysis Platform (BMGAP)

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Overview

BMGAP contains an analysis pipeline to identify and characterize bacterial meningitis pathogens using Illumina short-read sequencing, a database and API to store and serve analysis results, and a web-based UI to provide access to the results.

The BMGAP analysis pipeline requires Python 3.6+ as well as a number of dependencies, including BLAST+, MASH, and SPAdes. Data is stored in a MongoDB database, and is served using an ExpressJS-based server. The web UI is implemented using React.

The BMGAP analysis pipeline includes several purpose-built analysis tools, including BMScan, which uses MASH and a custom database to provide species identification for bacterial meningitis pathogens, LocusExtractor, which uses PubMLST references to identify MLSTs for both Neisseria sp. and Haemophilus influenzae, and PMGA, which identifies and annotates serogrouping/serotyping genes and MLST alleles.

Access to BMGAP through the OAMD Portal

BMGAP can be accessed online through the OAMD Portal (amdportal-sams.cdc.gov). To request access to BMGAP, please contact the BMGAP team at Shalabh Sharma - [email protected] to register for using the OAMD Portal.

Additional details on the account creation process can be found in the SAMS User Guide: [https://auth.cdc.gov/sams/SAMSUserGuide.pdf?disp=true].

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