MetaPhlAn4

What does it do?

MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequence data.

For more information, see the MetaPhlAn 4.0 website, and/or the tutorial describing use of MetaPhlAn.

If you publish data using this automator, don't forget to cite the authors of the tool Blanco-Míguez et al., 2023.

How do I use it?

Subject

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

Description

Required Components

You must include the type(s) of sequence(s) (fastas, fastqs, nanoporefastqs), each followed by a list of desired SEQIDs - one per line. For example, in the description:

fastqs
2023-SEQ-0415
2023-SEQ-0414
fastas
2025-MIN-0333

The automator will parse through the provided list, and run the analysis on the specified sequence types.

IF you would like to analyse both an assembly/fasta, AND the raw data, you MUST list the SEQID under BOTH sequence types

Optional Components

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

  • analysis - By default, MetaPhlAn4 automator will run analysis for relative abundance with read stats.
    • default is rel_ab_w_read_stats - profiling a metagenomes in terms of relative abundances and estimate the number of reads coming from each clade
    • If you want a different analysis, add the following line:
      • analysis=rel_ab - profiling a metagenome in terms of relative abundances
      • analysis=clade_profiles - normalized marker counts for clades with at least a non-null marker
      • analysis=marker_ab_table - normalized marker counts
      • analysis=marker_pres_table - list of markers present in the sample

Example

For an example MetaPhlAn4 analysis, see issue 37794. The zip file has been attached to this request as an example (the dropbox links expire after approx. 2 weeks).

Interpreting Results

MetaPhlAn4 will upload a zipped folder called metaphlan4_output_redmineID.zip to the ftp once it has completed. This will contain report files for MetaPhlAn4 and bracken analyses.

How long does it take?

The time required for analysis will depend on the analysis type and number of sequences requested.

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

Default database version is currently mpa_vJan25_CHOCOPhlAnSGB_202503. If you would like a different database version, please contact the bioinformatics team.