fastani
Tags: ani average-nucleotide-identity taxonomy species comparison run-scope
Calculate Average Nucleotide Identity (ANI) between genomes.
This subworkflow uses FastANI to compute whole-genome Average Nucleotide Identity (ANI) values between query genomes and reference genomes. ANI is a robust measure of genomic similarity used for species delineation in microbial taxonomy. The results are aggregated into a single consolidated report.
Take
query: Channel<Record>
reference: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
fna | Query genomes in FASTA format for ANI calculation |
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
fna | Reference genomes in FASTA format for ANI calculation |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
| Output | Description |
|---|---|
tsv | A tab-delimited summary of the ANI scores, matched fragments, and total fragments |
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- fastani - Compute whole-genome Average Nucleotide Identity (ANI).
Used By
This subworkflow is used by the following 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)