Remove and Annotate with Unique Molecular Index

During library preparation of the samples with a QIAseq Targeted DNA Panel, a UMI and a common sequence prefix are added to each read before amplification. While the UMI is essential in identifying reads that originate from the same fragment, retaining it as such on the sequenced reads would hinder the subsequent read mapping efficiency and accuracy. Therefore, the Remove and Annotate with Unique Molecular Index tool removes the UMI and the common sequence prefix from the reads, while annotating each read with the UMI to retain the fragment identity as annotation.

The tool can be found in the Toolbox here:

        Tools | QIAseq Panel Expert Tools (Image qiaseq_expert_folder_closed_16_n_p) | QIAseq DNA Panel Expert Tools (Image qiaseqv3_folder_open_16_h_p) | Remove and Annotate with Unique Molecular Index (Image add_remove_molbarcode_16_h_p)

In the first dialog (figure 5.34), select the reads saved as a sequence list.

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Figure 5.34: Select the reads generated using the QIAseq DNA Panel.

In the Settings dialog (figure 5.35), the following options are available.

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Figure 5.35: Settings.

Click Next to choose whether to Open or Save your results. By default (i.e., with the Common sequence verification option unchecked), the tool outputs the same number of reads as was present in the input, where reads have had their UMI and common sequence trimmed off. It is also possible to output a report that will inform about the total number of reads processed, the total number of reads found to have UMIs and the fraction of reads that have UMIs.