chewBBACA

Getting Started

  • Overview
  • Important Notes
  • Useful links
  • Installation
  • Quick Start

User Guide

  • CreateSchema - Create a gene-by-gene schema
  • AlleleCall - Determine the allelic profiles of a set of genomes
  • SchemaEvaluator - Build an interactive report for schema evaluation
  • AlleleCallEvaluator - Build an interactive report for allele calling results evaluation
  • ExtractCgMLST - Determine the set of loci that constitute the core genome
  • RemoveGenes - Remove a set of loci from allele calling results
  • PrepExternalSchema - Adapt an external schema to be used with chewBBACA
  • JoinProfiles - Join allele calling results from different runs
  • UniprotFinder - Retrieve annotations for loci in a schema
  • DownloadSchema - Download a schema from Chewie-NS
  • LoadSchema - Upload a schema to Chewie-NS
  • SyncSchema - Synchronize a schema with its remote version in Chewie-NS
  • NSStats - Retrieve basic information about the species and schemas in Chewie-NS

Tutorials

  • Step-by-step Tutorial
  • Integration with Chewie-NS

Help and support

  • Contacts
  • FAQ
chewBBACA
  • Useful links
  • View page source

Useful links

  • Look through the list of schemas in Chewie-NS. Chewie-NS allows chewBBACA users to download and update cg/wgMLST schemas, allowing the easy sharing of results, while ensuring the reproducibility and consistency of these steps.

  • A ready to use docker image automatically built from the latest version of chewBBACA in Ubuntu 22.04.

  • chewBBACA is available as a Galaxy module. Many thanks to Stefano Morabito and Arnold Knijn for EURL VTEC in ISS, Rome!

  • Check our Changelog to know more about the latest changes!

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