PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw re

[chayan]

Which utility package (preferable web-based) is available to generate PCA plots based on nucleotide word frequency (k-mer) of assembled contigs &/or raw reads ??? I found R bit tricky and tough to handle...so any thing other than R or R with some really helpful guide is preferable...

[gringer]

FactoMineR does a lot of great PCA things, and can fairly easily produce nice plots:

http://factominer.free.fr/classical-methods/principal-components-analysis.html

According to the FactoMineR main page, there's also now Factoshiny, which provides a dynamic, interactive way to explore your data with FactoMineR:

http://factominer.free.fr/

I found R bit tricky and tough to handle...so any thing other than R or R with some really helpful guide is preferable

You're posting in a bioinformatics forum, and rubbishing the free software swiss army statistics chainsaw of R. Saying "R is too confusing, can you tell me how I can do [statistics] without using R" is unlikely to give you good results.

[chayan]

No not at all rubbishing..sorry if I misunderstood...i just said as i am not a bioinformatician so i found it tough to use..anyway thanks for your suggestion

[cliffbeall]

Since this is one of the top hits while googling, thought I would leave here that CheckM with the tetra_pca command will do this:

https://github.com/Ecogenomics/CheckM/wiki/Plots