Standalone HTML Interactive Coverage Plot (SHICP)

The tool generates the HTML Interactive Coverage Plot given coverage depth information, variants and DNA gene features.

Dependencies

Software Version

• The tool is still in the development phases with current version is 1.0.0dev

Programming Languages

• Python (>= 3.6)
• HTML/CSS/Javascript

Tools/Libraries

• Echarts
• Python libraries: Biopython, rich, typer, pandas
• select2
• jinja2

Usage

Prepare Samples Data

The tsv file of samples data (samples.tsv) is as follow. Note that no header is needed

Sample-01	path/to/sample-01-coverage-depth	path/to/sample-01-variant-vcf
Sample-02	path/to/sample-02-coverage-depth	path/to/sample-02-variant-vcf
Sample-03	path/to/sample-03-coverage-depth	path/to/sample-03-variant-vcf

Others data

• Reference Sequences (reference.fasta)
• Genbank file contains gene features (sequence_genbank.gb)

Output

The tool will generate the Coverage Plot for samples in HTML file

Command

shicp -s samples.tsv -r reference.fasta -o sequencing_coverage_plot.html -g sequence_genbank.gb

HTML File Structure

• Chart Options Tab: allows user to customize chart display such as select which samples to be displayed, set datazoom, tooltips
• Coverage Plot Tab: displays Coverage Plot for selected samples in which user can do interactive oprerations such as zoom in/out, view for specific regions ect...
• Summary Information Tab: displays summary information for all samples included in an analysis
• About Tab: Sofware information, user guide

Author

• Development Lead: Peter Kruczkiewicz (peter.kruczkiewicz@gmail.com)
• Software Developer: Hai Nguyen (nhhaidee@gmail.com)

License

© 2021 Canadian Food Inspection Agency of Canada, Government of Canada.

Distributed under the MIT license.

What happens when the number of samples shown on the chart changed?

• By the default, at first up to 3 first samples are selected for displaying on the charts
• The entire chart will be re-rendered if you select/change samples to be displayed and you need to set your chart options again, changing other options will not re-render the entire chart

What happens when browser zoom is set more than 100%?

• Some minor graphic (such as some items get cut off) issues may happen. To fix this type of issue, try to adjust browser zoom and this may allow you to have better view

How many simultaneous samples are on the chart for the best view?

• It is recommended that having around 5 simultaneous samples on the chart for the best view

What will you do when the plot is distorted or minimized?

• This issue could happen when you shrink and maximize browser, to restore plot display just simply refresh browser