Browsing Virome Sequencing Analysis Results"

How to use the Virome Browser

Before you start

The Virome Browser shiny app makes it easy to import, filter and browse results generated from virome NGS data. The result files necessary to use the viromebrowser app are contig files, tabular formatted contig annotation files, read mapping files.

R version 3.6.3 was used for the development of the Viromebrowser, R version 4.0.0 or later has not been tested. To run the viromeBrowser Rstudio version 1.2.5033 or later is recommended.

Getting started

Run the following code to start the Virome Browser app locally on your computer:


This will start the Shiny app server and will indicate from what local address the app can be reached (e.g. by default) Alternatively you can host the app at a specific IP-address and port by specifying the host and port parameters of the viromeBrowser() function.

If R complains that the packages Biostrings and/or Rsamtools have not been installed install them with these commands:

if (!requireNamespace("BiocManager", quietly = TRUE))


Loading data into the Virome Browser

Four types of files must be loaded in the app:

After loading all the files press the "Load Data" button to start processing the files.


After loading the data (wait for the loading bars to disappear) the tables under the panel "Metadata", "Annotation Files", "Contig Files" and "BAM Files" will be filled. These tables can be used to check whether the imported data was loaded correctly.

Two new menu items will also appear in the sidebar on the left, click on the "Interactive Data Browser" tab to continue.

Filtering and selecting annotation results using the interactive data browser

There are three ways of filtering the annotation results:


After filtering and making a selection of annotations and samples, the next step is to either download the selected contigs or further inspect the contigs in the "selected sequence annotations" menu.

Saving selected contigs

The table in "selected sequence annotations" part of the app shows the selected contigs based on the defined filter settings and their taxonomic lineage determined by calculating the lowest common ancestor for contigs with multiple annotations.


You can select one or multiple lines of the table and click on "Download Selected Contigs" in the bottom of the screen to download the selected contigs. Use the "Download All Filtered Contigs" button to download all contigs in the current table (This can take a while to process with a large number of contigs).

In addition, it is possible to inspect the selected contigs by clicking the "Contig Information" tab.

Inspecting annotated contigs

The contig information tab shows you the annotation information of the selected contigs. Additionally a simple open reading frame prediction is performed by finding all canonical stop codons in all six frames of the contig. The predicted ORFs are displayed in the graph in the bottom. You can set a minimal ORF size limit with the slider.

Clicking the magnification glass in the graph allows you to zoom in and out. The two black lines indicate what part of the sequence has been annotated.

The "ORF Information" tab can be selected to further inspect the predicted open reading frames.


Inspecting open reading frames

In the ORF information tab you can select and visualize the ORF sequence, translate it and look at the amino acid characteristics of the sequence. The sliding window size slider determines the sliding window size over which a density is calculated and displayed in the heatmap in the bottom. By clicking the "Collect ORFs" button you can add all predicted ORFs to a download list.

Click the "Sequence collection table" tab to continue


Downloading collected open reading frames

After collecting ORF sequences you can download the sequences of these ORFs as nucleotide or as amino acid fasta file by clicking the "Download Fasta" button. If you would like to clear the table, click the "Clear Collection" button.


Try the viromeBrowser package in your browser

Any scripts or data that you put into this service are public.

viromeBrowser documentation built on April 7, 2021, 5:09 p.m.