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 a list of SEQIDs one per line.

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=reads_map - mapping from reads to clades (only reads hitting a marker)
      • analysis=clade_profiles - normalized marker counts for clades with at least a non-null marker
      • analysis=marker_ab_table - normalized marker counts
      • analysis=marker_counts - non-normalized marker counts [use with extreme caution]
      • analysis=marker_pres_table - list of markers present in the sample

Example

For an example MetaPhlAn4 analysis, see issue 30290. The zip file has been attached to this request as an example (the ftp 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

MetaPhlAn version 4.0.6 (as of 2024-07-03)

Default database version is currently mpa_vOct22_CHOCOPhlAnSGB_202212