mash_dist

Tags: mash distance minhash ani comparison taxonomy sample-scope

Calculate genomic distances using MinHash sketches.

Uses Mash to compute the distance between query sequences and a reference database. It uses MinHash sketches to rapidly estimate the Jaccard index, providing a fast approximation of Average Nucleotide Identity (ANI).

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	FASTA, FASTQ, or Mash sketch file to be queried

reference: Path

Name	Type	Description
reference	Path	The reference file (FASTA, FASTQ, or Mash sketch) to compare against

Outputs

record (
    meta: Record,
    dist: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
dist	Path	A tab-delimited summary of the Mash distances and p-values
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

mashdist Parameters

Parameter	Type	Default	Description
--mash_sketch	string		The reference sequence as a Mash Sketch (.msh file)
--full_merlin	boolean	false	Go full Merlin and run all species-specific tools, no matter the Mash distance

Used By

Subworkflows

• mashdist - Calculate Mash distances between sequences and a reference.

Workflows

• mashdist - Calculate Mash distances between sequences and reference genomes.

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)

Source

View source on GitHub

Version

MASH_DIST:
    - mash: 2.3