ANI calculation: alternatives to Jspecies

Question

[fhsantanna]

I am trying to calculate ANI values (ANIm and ANIb) using Jspecies in Ubuntu 14.04.

For the majority of comparisons, Jspecies is not able to attribute a ANI value (instead it gives "nan" result). Funny is that sometimes it works well.

Here is the log when errors occur:

[12:57]ERROR509909[Thread-11] - api.calculation.anim.RunANIm.calculateEMA(RunANIm.java:75) - .cluster file doesn't exist # seems to be related to nucmer
[12:58]ERROR580395[Thread-11] - api.calculation.blast.FormatDB.runFormatDB(FormatDB.java:61) - [formatdb] FATAL ERROR: Database base name must be provided with multiple input files

Do you know an alternative software to jspecies?

Thanks

[dago]

I discovered this http://jspecies.ribohost.com/jspeciesws/

Apparently they moved on the web. Maybe it can help you.

[fhsantanna]

Great! Thank you very much. I am going to give it a try.

[dago]

Let me understand, you submit different file in Jspecies and sometimes it works and sometimes not. Is that right?

[fhsantanna]

Yes. I was not able to figure out what is the problem. Maybe it is a incompatibility with the new version of blast, because when I utilize an script for ani calculation, blast crashes sometimes...

[dago]

I had a similar problem. Are you in Linux system? Did you import the files from windows? Which blast version are you using?

[fhsantanna]

Yes, I am using Linux (Ubuntu 14.04). No, I didn' t import files from windows. Blastall version 2.2.26.

[dago]

If I am not wrong ANIm uses mummer, does mummer work in your system? for the formatdb error, maybe it does not like the Ids of you seqs. You could give it a tray using one string, no space, only alphanumeric characters e.g. > MYSEQUENCE

Answer 1

[aleimba]

An alternative that I can highly recommend is pyani from Leighton Pritchard. No GUI just command-line, but that was one of the major drawbacks of the Java JSpecies anyway. Therefore, pyani can handle lots of microbial genomes at once.

https://github.com/widdowquinn/pyani

Additionally, pyani can also create heatmap diagrams corresponding to the ANI or Tetra values with a hierarchical clustering of the results (with additional QC graphics).

pyani relies heavily on some very common Python libraries and R or matplotlib for graphical output, but most bioinformaticians will have these installed anyway.

Answer 2

[Raul]

Problem using pyani: after a few years I am trying to use pyani again. I read the info at https://pypi.org/project/pyani Installed it in one of my conda environments It runs, but it fails to complete the analysis since it uses "from_csv" to import pandas and it is deprecated https://itecnote.com/tecnote/python-no-from_csv-method-in-pandas/ "from_csv is deprecated. Please use read_csv(...) instead. Note that some of the default arguments are different, so please refer to the documentation for from_csv when changing your function calls"

Answer 3

[colindaven]

I used fastANI successfully a couple of years ago. It is still under active development.

https://github.com/ParBLiSS/FastANI