Heatmap visualisation tool for viral metagenomic data
AllmondViz is a way of displaying viral metagenomic data in heatmap form.
It can be used as a way of visualising viral diversity, along with multiple other sorting options, within a sample or between multiple samples.
AllmondViz is designed to follow on from the Allmond metagenomic pipeline (https://github.com/rjorton/Allmond) which does the following:
1. Sequencing of metagenomic sample<br>
2. Trimming of reads<br>
3. Alignment of reads against host to remove host reads<br>
4. Remove bacteria reads with DIAMOND blastx<br>
5. De novo assembly of reads into contigs<br>
6. Classification of contigs using DIAMOND blastx<br>
7. File extended to include taxonID, length, family name and genus name<br></font size="5">
-Display by either Family or Genus
-Sort by contig length, number of contigs, evalue and percentage of genome size
-Clustering based on contigs present
-Different colour schemes
-View contigs by clicking on elements of the heatmap and extracting the sequences of these contigs by selecting the contig file
-Option to exlude contigs under a specified length, bacteriophages and anything that does not infect invertebrates
-Saving the heatmap image
Input is a tab delimited text file with 16 columns<br>
Contig ID | Seq-ID | % Identical Matches | Alignment Length | No. Mismatches | No. Gap Openings | Start(query) | End(qeury) | Start(subject) | End(subject) | eValue | Bit Score | TaxonID | Contig Length | Family Name | Genus Name |
First click the 'Open' button and select the Allmond pipeline output files. This will display the data in heatmap form. To add extra samples in click the 'Add' button.
To change how the data is scaled/the colouring/exclude contigs, select the desired options from the left hand panel.
To save the heatmap image in PNG format, click the 'Save' button at the bottom of the GUI.
To view the contigs represented by a rectangle, either hover the mouse over it. To display them on the side panel, click on the rectangle.
To save these contigs as a text file list, click the 'Export contigs' button.
To reset the heatmap and clear the display, click the 'Reset' button.