bactopia_datasets

Tags: download database setup amr mlst minhash sourmash gtdb run-scope

Download pre-compiled datasets required by Bactopia.

Fetches the core datasets (AMR, MLST, Mash, Sourmash) hosted by the Bactopia project. These are used to populate the local cache for offline use.

Internet Required

This process requires an active internet connection to fetch files from datasets.bactopia.com.

Outputs

record (
    amrfinderplus_db: Path,
    mlst_db: Path,
    mash_db: Path,
    sourmash_db: Path
)

Field	Type	Description
`amrfinderplus_db`	`Path`	A compressed tarball of the AMRFinderPlus database
`mlst_db`	`Path`	A compressed tarball of the PubMLST schemes
`mash_db`	`Path`	Pre-computed Mash sketches (RefSeq)
`sourmash_db`	`Path`	Pre-computed Sourmash signatures (GTDB)

bactopia_datasets - Download and provide pre-compiled datasets required by Bactopia.

amrfinderplus - Bactopia Tool: Amrfinderplus.
bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
merlin - MinMER-assisted species-specific tool selection and execution.
staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.

If you use this in your analysis, please cite the following.

Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)
AMRFinderPlus
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu C-H, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrob. Agents Chemother. (2019)
mlst
Seemann T mlst: scan contig files against PubMLST typing schemes (GitHub)
Mash
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 17, 132 (2016)
Sourmash
Brown CT, Irber L sourmash: a library for MinHash sketching of DNA. JOSS 1, 27 (2016)

BACTOPIA_DATASETS:
    - gnu-wget: 1.18