Data QC and Taxonomic Profiling

The Data QC and Taxonomic Profiling combines the Taxonomic Profiling tool with a trimming step and additionally creates sequencing QC reports. The workflow outputs a taxonomic profiling abundance table as well as additional reports on the trimming, QC and taxonomic analysis.

To run the tool, go to:

        Toolbox | Template Workflows (Image workflow_group) | Microbial Workflows (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Taxonomic Analysis (Image taxonomic_analysis_folder_closed_16_n_p) | Data QC and Taxonomic Profiling (Image data_qc_taxprofile_16_n_p)

You can select only one read file to analyze (figure 3.14). Alternatively, multiple files can be run using the batch mode.

Image taxpro_1_wf
Figure 3.14: Select the reads to analyze.

In the "Trim Sequences" dialog, you can specify a trim adapter list and set up parameters if you would like to trim your sequences from adapters. Specifying a trim adapter list is optional but recommended to ensure the highest quality data for your typing analysis (figure 3.15).

Image taxpro_2_wf
Figure 3.15: You can choose to trim adapter sequences from your sequencing reads.

The parameters that can be set are:

In the "Taxonomic Profiling" dialog (figure 3.16), choose the list of references that you wish to map the reads against. You could also remove host DNA by specifying a reference genome for the host (in the case of human microbiota, the Homo sapiens GRCh38 for example). The reference database can be obtained by using the Download Curated Microbial Reference Database tool (Download Curated Microbial Reference Database) or Download Custom Microbial Reference Database tool (Download Custom Microbial Reference Database). The host index and (if using the custom downloader) the microbial reference index are built with the Create Taxonomic Profiling Index tool (Create Taxonomic Profiling Index).

Image taxpro_3_wf
Figure 3.16: Specify the reference database. You can also check the option "Filter host reads" and specify the host genome.

The abundance table displays the names of the identified taxa (possibly with their underlying assemblies), along with their full taxonomy, the total amount of reads associated with that taxon, the total number of reads associated with the children of that taxon, and a coverage estimate. The table can be visualized using the Stacked bar charts and stacked area charts function, as well as the Sunburst charts (see Taxonomic profiling abundance table).

The Taxonomic Profiling report is divided in three sections:

In addition, it generates three reports: a trimming report, a graphical QC report and a supplementary QC report. All of these should be inspected in order to determine whether the quality of the sequencing reads and the trimming are acceptable. For a detailed description of the QC reports and indication on how to interpret the different values, see

For the trimming report, see