Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Here are a few tips for Pavian to work with large data.
E.g., Maximum upload 50M files for Pavian, simple input:
- Besides M (megabyte), B (byte), K (kilobyte) and G (gigabyte) also supported.
- This option is defined in the script runApp.R in Pavian source.
Clone the Pavian repository locally
git clone https://github.com/fbreitwieser/pavian.git
In line 72, modify pavian.maxFiles from 100 to 1000.
Then start R
Next install modified repository as Pavian and run the shiny app: