BacQuerya is a search engine for genomic metadata for bacterial pathogens. BacQuerya is built using React.js and is currently in beta. The gene and sequence searches on include S. pneumoniae genomic metadata at this time.
The BacQuerya-processing pipeline (https://github.com/bacpop/BacQuerya-processing) sources genomic metadata from several public repositories that include: NCBI GenBank, BioSample, the European Nucleotide Archive and the Sequence Read Archive. Metadata from each of these sources is extracted and combined into a JSON document, that is then indexed using Elastic cloud (https://www.elastic.co) and is searchable from the BacQuerya website.
We also conduct a number of pre-processing steps and include the outputs of these in the indexed metadata when appropriate. These include: evaluation of assembly quality, gene annotation (using population reference graphs and Pfam searches) and multiple sequence alignment (using the Partree algorithm in the MAFFT package).
The BacQuerya-API (https://github.com/bacpop/BacQuerya-api) is the backend server for the website, and used to conduct all index querying and additional user requests.
The BacQuerya website was developed by Daniel Anderson, John Lees and Jeffrey Sweeney.
In the project directory, you can run:
Runs the app in the development mode.
Open http://localhost:3000 to view it in the browser.
The page will reload if you make edits.
You will also see any lint errors in the console.