AllTheBacteria documentation

All WGS isolate bacterial INSDC data to August 2024 uniformly assembled, QC-ed, annotated, searchable.

Follow up to Grace Blackwell’s 661k dataset (which covered everything to Nov 2018).

Preprint: https://doi.org/10.1101/2024.03.08.584059

Please use the github repository to raise any issues: https://github.com/AllTheBacteria/AllTheBacteria/issues

Contents:

• Overview
  • Current status
  • Where are the docs/data/methods?
  • Releases
  • A brief history of AllTheBacteria
  • Future releases
• Metadata and QC
  • Metadata in flat files and SQLite database
  • Metadata in flat files
  • Older data
  • Metadata files
• SQLite metadata
  • Background
  • Metadata checks
  • SQLite database
  • Example SQLite queries
• Assemblies
  • Summary
  • Downloading assemblies from AWS
  • Downloading assemblies from the ENA
  • Downloading assemblies from OSF
  • Species calls and assembly batches
• Species identification
• Annotation
  • Bakta
• Antimicrobial Resistance
  • AMRFinderPlus
• Biosynthetic Gene Clusters
  • GECCO
• Species specific typing
  • Summary
• Archaea
• Sequence alignment with LexicMap
  • ​Searching on AWS EC2
  • Local search with pre-built index
  • Building an index and searching locally
• Contributing to AllTheBacteria
  • Background information
  • Making your analyses reproducible
  • SOP for contributing
• Batch downloading from OSF
  • All latest files
  • Making file lists
• FAQ
  • Can I freely use the data?
  • How can I get involved?
  • What happens if two people want to run their competing methods?
• Release History
  • Release Version 0.1
  • Release Version 0.2
  • Incremental release 2024-08
• Migration from EBI FTP to OSF
  • Spare me the details, I just want old -> new names
  • What was/is on the EBI FTP site?
  • What is on OSF?
  • Metadata files
  • Assembly files
  • Index files
  • Are 15 Phylign files missing?