Kraken2

What does it do?

Kraken2 is a program for taxonomic sequence classification.

For more information, see the Kraken2 github, and/or the protocol paper describing use of Kraken2.

If you publish data using this automator, don't forget to cite the authors of the tool Wood and Salzberg, 2014 and the Kraken2 paper Wood et al., 2019

How do I use it?

Subject

In the Subject field, put kraken2. Spelling counts, but case sensitivity doesn't.

Description

Required Components

You must include a list of SEQIDs one per line.

Optional Components

In order to customise your analyses, additional settings can be optionally modified:

  • seqtype - By default, the Kraken2 will assume you are running an analysis on paired-end raw sequence data.

    • default is paired
    • If you want to analyse long-read nanopore or assembly data, add the following line:
      • seqtype=nanopore
      • seqtype=assembly

  • database - the default analysis will utilize the Kraken2 standard database (9/26/2022) from Kraken2 index zone.

    • default is kraken2
    • If you want to analyse using a different database, the following options are currently supported:
      • database=greengenes
      • database=plusPF
      • database=rdp
      • database=silva

    -The kraken2 and plusPF databases are meant for metagenomes, all others are 16S based databases

Example

For an example kraken2 analysis, see issue 29355. The zip file has been attached to this request as an example (the ftp links expire after approx. 2 weeks).

Interpreting Results

Kraken2 will upload a zipped folder called kraken2_output_redmineID.zip to the ftp once it has completed. This will contain report files for kraken2 and bracken analyses.

How long does it take?

Kraken2 is much faster than the original kraken, however the time required for analysis will depend on the analysis type and number of sequences requested. If too many sequences are requested at once, the automator may run out of memory and fail. Please try to keep it to 10 metagenomes maximum.

What can go wrong?

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.

Version

Version 2.1.2 is currently available at the OLC. (as of 2024-07-4)