open-data-registry/datasets/allthebacteria.yaml at main · awslabs/open-data-registry · GitHub

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Name: AllTheBacteria
Description: All bacterial isolate whole-genome sequencing data from INSDC, uniformly assembled, quality-controlled, annotated, and searchable.
Documentation: https://allthebacteria.org
Contact: https://github.com/AllTheBacteria/AllTheBacteria/issues
ManagedBy: "[European Bioinformatics Institute](https://www.ebi.ac.uk/)"
UpdateFrequency: |
  The current release is for all SRA bacterial isolate data up to August 2024. The
  colllection will be updated occasionally, with no fixed schedule.
Tags:
  - assembly
  - bacteria
  - bioinformatics
  - fasta
  - genomic
  - life sciences
  - microbial genomics
  - short read sequencing
  - whole genome sequencing
License: "[MIT License](https://opensource.org/license/mit)"
Resources:
  - Description: Individual, compressed genome assemblies in .fasta format in a public S3 bucket.
    ARN: arn:aws:s3:::allthebacteria-assemblies
    Region: eu-west-2
    Type: S3 Bucket
    Explore:
  - Description: Phylogenetically-compressed, batched xz archives of all genome assemblies in .fasta format in a public S3 bucket.
    ARN: arn:aws:s3:::allthebacteria-phylogeneticbatches
    Region: eu-west-2
    Type: S3 Bucket
    Explore:
  - Description: Metadata for each genome assembly, including taxonomic information, in a public S3 bucket.
    ARN: arn:aws:s3:::allthebacteria-metadata
    Region: eu-west-2
    Type: S3 Bucket
    Explore:
  - Description: "A [LexicMap](https://github.com/shenwei356/LexicMap) index of all genome assemblies. This can be used for efficient sequence alignment against all genomes."
    ARN: arn:aws:s3:::allthebacteria-lexicmap
    Region: eu-west-2
    Type: S3 Bucket
    Explore:
DataAtWork:
  Publications:
    - Title: AllTheBacteria - all bacterial genomes assembled, available and searchable
      URL: https://doi.org/10.1101/2024.03.08.584059
      AuthorName: Hunt M, Lima L, Anderson D, Hawkey J, Shen W, Lees J, Iqbal I
      AuthorURL: https://researchportal.bath.ac.uk/en/persons/zamin-iqbal
ADXCategories:
  - Healthcare & Life Sciences Data