v2.0.1

Variant Hunter is even more versatile

This minor update brings with it several improvements that allow for greater flexibility of use.

 

🚀   Features

• Introduction to lineage-specific analyses with multiple lineages: you can now select multiple lineages in lineage-specific analyses. More: you can select entire branches of lineages by selecting values such as BA.1.* . To sum up: you can filter sequences by, for example, selecting BA.1, or BA.1 and BA.2, or BA.1.*, or BA.1.* and BA.2.*. In short, anything you want!

• New speed Heat map: a new heat map view allows you to discover the fastest growing mutations at a glance

• Links: now you can create a link to an analysis and share it

• App tour and quick start examples: new to Variant Hunter? No problem, a step-by-step guide will walk you through the tool. And you can also run featured examples.

 

🔧   Fixes

• Improved screen capture

• Updates to the about section

v2.0.0

Variant Hunter has a new look!

Variant Hunter has a new look and brings with it many new features.
The user experience has been redesigned from the ground up to provide improved usability, greater flexibility, many new features, and even better performance.

 

🚀   Features

• New design: the new interface separates the results from the analysis creation panel. You no longer have to move up and down.

• App sidebar: now you can move easily from one analysis to another thanks to the brand new pop-up sidebar. Agility is the watchword. And you can also filter past analyses by granularity, type, tag, and favorite.

• Pick up where you left off: now the application keeps all your data stored in your browser. You no longer have to redo everything every time

• Simpler analysis definition panel: creating a new analysis is easier than ever. New explanatory labels help the user in defining parameters.

• Introduction to tags: it is now possible to associate a tag to each analysis. Tags allow you to group past analyses. But there is more: indeed, tags allow you to preserve filtering and sorting options between various analyses. So you can apply the same filters to an entire group of analyses. Fast, isn't it?

• New speed Heat map: a new heat map view allows you to discover the fastest growing mutations at a glance

• Filtering scopes: in addition to tag-based filtering, it is always possible to switch to a local scope. This gives you the flexibility to drill down into a specific analysis within a tag group without changing the filters associated with the entire analysis group. So versatile!

• Results toolbar: a new toolbar in the results panel allows you to keep an eye on analysis parameters at any time. It also provides very handy controls for adjusting search parameters, marking the analysis as favorite or deleting it.

• Quick adjustment of analysis parameters: with the brand new controls in the toolbar you can quickly and easily change the analysis parameters. For example you can move from lineage-specific to lineage-independent search; move to a larger geographic area (from region to country to continent); and you can also shift the analysis period (by one or two weeks). Analyses generated in this way are automatically assigned to a tag group, if not already assigned.

• Introduction to notes: what was interesting about the trend of this old analysis from last week? Now you can write it in the notes section. All clearer.

• Mutation report: it often happens to filter by selecting a large number of mutations, but how to quickly figure out which ones are missing and which ones are not? Now things are easier with the mutation report. The green ones are there, the red ones are not. Clear, isn't it?

• Analysis metadata: each search panel now includes a final section where some metadata is visible: a summary about the search parameters, when you performed it, on which dataset, your notes, and the associated tag.

• Improved UX: colors, labels, text and icons will assist you in the analysis process.

• It gets dark: dark mode is here and it's even automatic.

• Keyboard shortcuts: ctrl + N to create a new analysis; ctrl + arrow up to go to the next analysis; ctrl + arrow down for the previous one.

 

🚧   Under the hood

• Robustness: Variant Hunter is no longer scared of format changes in the metadata.tsv files. It can now automatically determine the position of columns of interest. Gisaid and Nextstrain, you are warned!

• Caching HTTP requests: now all requests to the server are chached locally, so everything is more efficient.

• Improved performance: the app is now faster thanks to the all-new design that requires far fewer resources.

• Better code organization

 

🔧   Fixes

• Improved screen capture

v1.1.0

🚀   Features

• Dynamic location selector: it is now possible to select the location directly by typing its name or by proceeding in an 'exploratory' manner by adding a slash after the name of the continent and/or country (or by clicking on the completion arrow in the results). For example, Lombardy can be found with "Lombardy" or with "Italy/" or "Europe/Italy/";
• Added functionality to switch between weeks also at top of tabs;
• Added license section in /about;
• Simplified the mutation table (by removing Locations);
• Aggregation of lineages: it is now possible to aggregate lineages in the expansion panel of a mutation. Aggregation is available at two levels: level 1 (BA.1.* ) and level 2 (BA.1.1*). In any case, relevant lineages are not aggregated (those with at least 10% in at least one of the 4 weeks);
• Integration of covSPECTRUM: It is now possible, by selecting mutations from the table, to generate a search on covSPECTRUM for those mutations, in the same period and location as the current analysis (in the case of regional type analysis it switches to a country granularity, not being supported by covSPECTRUM). Currently not available for NSP proteins.
• Correction of p-values: p values related to frequencies are now corrected for multiple tests
• Mutation info panel: a new panel, accessible by pressing the 'i' on the mutation table, shows for the chosen mutation the list of lineages it has characterized (<=50% of sequences). It also reports the lineage decomposition of the sequences that exhibited that mutation.
• Minor UX improvements

🔧   Fixes

• Fixed minor issues

v1.0.0

Variant Hunter is here!

VariantHunter analyzes the frequencies of amino acid mutations of SARS-CoV-2 in order to observe interesting variant trends or identify novel emerging variants.

Features

VariantHunter supports two modes of analysis: Lineage Independent and Lineage Specific. Each mode allows to open several analysis sessions (managed in panels that can be expanded, collapsed, or deleted at the user's choice).

The underlying mechanism of both methodologies is the same: each amino acid mutation is analyzed for a time period of 4 weeks.
For each week, the frequency of the mutation (computed as "number of sequencing harboring the mutation"/"total number of sequences collected in that week") is considered; then, a linear model is fitted on the four data points.

The slope of the regression line represents how fast the mutation is growing (i.e., its percentage is increasing). Positive slopes indicate an increasing trend, while negative values of the slope indicate a decreasing trend.

Chi squared tests are computed to test the significance of the change of frequency of the mutation.

The main results of both analyses are summarized in a table of mutations, reporting their prevalence over the 4 weeks, their slope, and Chi squared tests p-values. In addition, different visualizations support the intuition of the observed trends of diffusion: a heatmap and various line-plots that represent prevalence or their odd ratios.