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The Taxonomic Profiling tool of the QIAGEN CLC Microbial Genomics Module can filter host reads from multiple organisms, but when multiple index files are provided as input, only the first is used to remove reads in versions of the software affected by this issue.
For example, if a virus database was chosen as the reference database, and two separate host index files for filtering out human reads and bacterial reads were provided, only the first host index would be used. If the human index file was the first in the list provided, this could result in bacterial reads contaminating the reads of interest, resulting in off-target alignments.
This issue was fixed in QIAGEN CLC Microbial Genomics Module 20.1.1. Please use this or a later version of the module.
Suggested work-arounds for this problem when using older versions of this product:
QIAGEN CLC Microbial Genomics Module 2.0 to 20.1.
This issue was fixed in QIAGEN CLC Microbial Genomics Module 20.1.1.