Mytax is a tool designed to utilize the Kraken2 <https://ccb.jhu.edu/software/kraken2/> classification tool in order to identify (and visualize) taxonomic designations of fastq files. It includes a flu-kraken (from JHUAPL) and minikraken (from developers of kraken) set of databases in the installed images.
Note
This module contains a UI to be displayed from the rendering button in the variables table
- fastq file : File
- FastQ file (single) obtained from any sequencing run. You can consolidate multiple fastq files into one if you want to run a long sequencing run.
- nodes : Directory
- Location of the taxonomy files. Default is contained within the
`jhuaplbio/basestack_mytaximage and pre-loaded on run - database : Directory
- Directory to use as the database for Kraken2. Defaults to Flukraken pre-loaded in the Docker image.
- memory-mapping` : Option
- Choose to pre-load the database (fast, requires high RAM) or run on the local filesystem (slow, only use with low RAM available)
- Kraken-Report File : .report
- Used in Pavian and for additional 3rd-party applications
- Contains a summary of the run
- Kraken-JSON : .json
- Formatted file uploaded/used in the Mytax Sunburst Visualization Procedure.
There are 2 primary procedures for this module:
- Create Report Files
- Run kraken-classify to create kraken.report and kraken.json files from a single fastq file
- View the Visualization
- View the output JSON file from Step 1
- Download and create/update custom databases
- Utilize other classifiers or aligners
