bactopia_sketcher

Tags: bacteria taxonomy classification minhash sketch mash sourmash refseq gtdb sample-scope

Create genomic sketches and perform rapid taxonomic classification.

Uses Mash and Sourmash to create MinHash sketches of the input sequences. These sketches are then queried against pre-built databases (RefSeq and GTDB to identify the closest reference genomes.

Databases Required

Requires the pre-compiled RefSeq (Mash) and GTDB (Sourmash) databases, usually downloaded by the datasets module.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

mash_db: Path
sourmash_db: Path

Name	Type	Description
mash_db	Path	Path to the Mash RefSeq database
sourmash_db	Path	Path to the Sourmash GTDB LCA database

Outputs

record (
    meta: Record,
    sig: Path,
    msh: Set<Path>,
    mash: Path,
    sourmash: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
sig	Path	The Sourmash signature file (*.sig)
msh	Set<Path>	The Mash sketch files for k=21 and k=31 (*.msh)
mash	Path	A classification report of Mash Screen results against RefSeq database
sourmash	Path	A classification report from Sourmash LCA against GTDB database
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Used By

Subworkflows

• bactopia_sketcher - Create genomic sketches and perform rapid taxonomic classification.

Workflows

• bactopia - Comprehensive bacterial analysis pipeline for complete genomic characterization.
• 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)

• 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)

• Mash Screen
  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)

• NCBI RefSeq Database
  O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O0, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733-45 (2016)

Source

View source on GitHub

Version

BACTOPIA_SKETCHER:
    - bactopia-sketcher: 1.0.3