Mytax

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

Parameters

fastq fileFile

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.

nodesDirectory

Location of the taxonomy files. Default is contained within the `jhuaplbio/basestack_mytax image and pre-loaded on run

databaseDirectory

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)

Returns

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.

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There are 2 primary procedures for this module:

1. Create Report Files

   • Run kraken-classify to create kraken.report and kraken.json files from a single fastq file

2. View the Visualization

   • View the output JSON file from Step 1

WIP Procedures

• Download and create/update custom databases

• Utilize other classifiers or aligners

  1. Centrifuge

  2. Kraken2

  3. BLAST

Display