Data QC and Remove Background Reads

The Data QC and Remove Background Reads workflow performs trimming of reads, creates a QC report and cleans the dataset from background DNA, leaving back only the reads that match the reference genome(s).

To run the Data QC and Remove Background Reads workflow, 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_16_n_p) | Data QC and Remove Background Reads (Image data_qc_clean_host_16_n_p)

You can select only one read file to analyze (figure 3.11). Alternatively, multiple files can be run using the batch mode.

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Figure 3.11: Select the reads. Use Batch mode if you have more than one set of reads.

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 (figure 3.12).

Image clean_2_wf
Figure 3.12: You can choose to trim adapter sequences from your sequencing reads.

The parameters that can be set are:

In the Taxonomic Profiling dialog, select the "Species of interest taxpro index" you will use to map the reads (figure 3.13). Here, you can also choose to "Filter background reads". You must then specify the "Background taxpro index" (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 clean_2
Figure 3.13: Select the reference databaes, and potentially a background taxpro index to remove possible contamination.

The workflow will output three sequence lists:

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