bactopia_datasets

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

Download and provide pre-compiled datasets required by Bactopia.

This subworkflow wraps the DATASETS module and extracts individual database paths as separate channel emissions for downstream consumption.

Emit

Published

The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.

Downstream Inputs

The following emissions are meant to be used as inputs to downstream subworkflows.

amrfinderplus_db

Path to the AMRFinderPlus database tarball

mlst_db

Path to the PubMLST database tarball

mash_db

Path to the Mash RefSeq sketch

sourmash_db

Path to the Sourmash GTDB signatures

Module Composition

This subworkflow calls the following modules:

• bactopia_datasets - Download pre-compiled datasets required by Bactopia.

Used By

This subworkflow is used by the following workflows:

• amrfinderplus - Bactopia Tool: Amrfinderplus.
• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• merlin - MinMER-assisted species-specific tool selection and execution.
• mlst - Automatic Multi-Locus Sequence Type (MLST) calling from assembled contigs.
• staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.

Citations

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)

• Mash Refseq (release 88) Sketch
  Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM Mash Screen: high-throughput sequence containment estimation for genome discovery Genome Biol 20, 232 (2019)

• PubMLST.org
  Jolley KA, Bray JE, Maiden MCJ Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3, 124 (2018)

• Sourmash Genbank LCA Signature
  Brown CT, Irber L sourmash: a library for MinHash sketching of DNA. JOSS 1, 27 (2016)

Source

View source on GitHub