fastani

Tags: fastani ani average-nucleotide-identity taxonomy genomic-distance comparison run-scope

Compute whole-genome Average Nucleotide Identity (ANI).

Uses FastANI to perform alignment-free computation of ANI between the input query genomes and a reference genome. This is the standard method for species definition (typically >95% ANI) and is much faster than traditional BLAST-based approaches.

Inputs

record (
    meta: Record,
    query: Set<Path>,
    reference: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
query	Set<Path>	One or more assembled contigs in FASTA format (Query genomes)
reference	Path	The reference genome assembly in FASTA format to compare against

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited summary of ANI scores, matched fragments, and total fragments
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

fastANI Parameters

Parameter	Type	Default	Description
--fastani_reference	string		Path to reference genome in FASTA format
--fastani_kmer	integer	16	kmer size (<= 16) for ANI calculation
--fastani_min_fraction	number	0.2	Minimum fraction of genome that must be shared for trusting ANI.
--fastani_frag_len	integer	3000	fragment length
--fastani_skip_pairwise	boolean	false	Only use RefSeq or local assemblies for ANI calculations

Used By

Subworkflows

• fastani - Calculate Average Nucleotide Identity (ANI) between genomes.

Workflows

• fastani - Fast alignment-free computation of whole-genome Average Nucleotide Identity.

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)

• FastANI
  Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018)

Source

View source on GitHub

Version

FASTANI:
    - fastani: 1.34