anvi-script-compute-ani-for-fasta
Run ANI between contigs in a single FASTA file.
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Authors
Requires
fasta 
Provides
genome-similarity 
Usage
This program computes the average nucleotide identity between reads in a single fasta file (using PyANI).
To compute the ANI (or other genome distance metrics) between two genomes in different fasta files, use anvi-compute-genome-similarity.
A default run of this program looks like this:
anvi-script-compute-ani-for-fasta -f fasta \
-o path/to/output \
--method ANIb
By default, the PyANI method is ANIb (which aligns 1020 nt fragments of your sequences using BLASTN+). You can switch to ANIm, ANIblastall, or TETRA if desired. See the PyANI documentation for more informaiton.
You also have the option to change the distance metric (from the default “euclidean”) or the linkage method (from the default “ward”) or provide a path to a log file for debug messages.
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-script-compute-ani-for-fasta.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
anvi-script-compute-ani-for-fasta [-h] -f FASTA file -o DIR_PATH [-p PAN_DB] [-T NUM_THREADS] [--log-file FILE_PATH] [--method {ANIm,ANIb,ANIblastall,TETRA}] [--distance DISTANCE_METRIC] [--linkage LINKAGE_METHOD] [--just-do-it]
Parameters and their descriptions
-f, --fasta-file FASTA FILE required- A FASTA-formatted input file.
-o, --output-dir DIR_PATH required- Directory path for output files
-p, --pan-db PAN_DB- Anvi'o pan database
-T, --num-threads NUM_THREADS- Maximum number of threads to use for multithreading whenever possible. Very conservatively, the default is 1, unless the environmental variable `ANVIO_THREADS` sets another positive integer. If you use this parameter, it will override `ANVIO_THREADS`. It is a good idea to not exceed the number of CPUs / cores on your system. Plus, please be careful with this option if you are running your commands on a SGE -- if you are clusterizing your runs, and asking for multiple threads to use, you may deplete your resources very fast. Default:
1
--log-file FILE_PATH- File path to store debug/output messages.
--method METHOD- Method for pyANI. The default is ANIb. You must have the necessary binary in path for whichever method you choose. According to the pyANI help for v0.2.7 at https://github.com/widdowquinn/pyani, the method 'ANIm' uses MUMmer (NUCmer) to align the input sequences. 'ANIb' uses BLASTN+ to align 1020nt fragments of the input sequences. 'ANIblastall': uses the legacy BLASTN to align 1020nt fragments Finally, 'TETRA': calculates tetranucleotide frequencies of each input sequence Choices:
ANIm ANIb ANIblastall TETRA Default: ANIb
--distance DISTANCE_METRIC- The distance metric for the hierarchical clustering. The default is "euclidean". Default:
euclidean
--linkage LINKAGE_METHOD- The linkage method for the hierarchical clustering. The default is "ward". Default:
ward
--just-do-it- Don't bother me with questions or warnings, just do it.
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.
