Welcome to VirMask

VirMask is a novel computational tool created to systematically mask non-viral elements (e.g., human, rRNA sequences and other artifacts) within viral reference databases, as well as virus-derived sequences that are recurrently detected in mNGS samples, likely introduced during sample preparation or sequencing workflows.

The ultimate goal of the tool is to improve reliability of viral mNGS diagnosis.

To see and download the code, visit our GitHub. Information on how to install the tool can be found in the Installation section.

VirMask consists of two main parts:

• Human masking: detects and masks viral refrence genomes that contain human sequences.

• Contaminants masking: identifies and masks recurrent contaminants within the viral database, such as rRNA seqences, vector contamination and sequencing adapters present in the viral database.

Users can run each of these two functions individually if only human sequences or recurrent contaminants need to be removed, or alternatively (and highly recommended), they can run VirMask as a whole:

• VirMask: spots and masks human sequences and recurrent contaminants from the viral database.

Some help can be obtained with VirMask.sh -h.

Enjoy using VirMask!