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Add some features that are missing from jbrowse 2 to the feature comparison table #1581

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Dec 23, 2020
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Add some features that are missing from jbrowse 2 to the feature comparison table #1581

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Add some features that are missing from jbrowse 2 to the feature comp…
cmdcolin Dec 22, 2020
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Add note on embeddability
cmdcolin Dec 23, 2020
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48 changes: 34 additions & 14 deletions website/src/pages/features.md
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Expand Up @@ -36,20 +36,23 @@ view types

## Feature comparison of JBrowse 2 vs JBrowse 1

| Feature | JBrowse 2 | JBrowse 1 |
| ------------------------------------------------------------------- | ----------------------- | --------- |
| Status updates during track loading (e.g. Downloading BAM index...) | :heavy_check_mark: | :x: |
| Uses webworkers for parsing and rendering tracks | :heavy_check_mark: | :x: |
| Supports interactive editing of configuration in the app | :heavy_check_mark: | :x: |
| Can "flip" or reverse complement the linear view | :heavy_check_mark: | :x: |
| Hi-C data rendering | :heavy_check_mark: | :x: |
| Can display multiple chromosomes in a single view | :heavy_check_mark: | :x: |
| Sort read pileup in alignments tracks | :heavy_check_mark: | :x: |
| Show soft clipping in alignments tracks | :heavy_check_mark: | :x: |
| Built-in spreadsheet-like view for datasets | :heavy_check_mark: | :x: |
| Can connect to UCSC track hubs | :heavy_check_mark: [^1] | :x: |
| Can load plugins at run-time instead of build time | :heavy_check_mark: [^2] | :x: |
| Non-admin users can open tracks and share them with others | :heavy_check_mark: [^3] | :x: |
| Feature | JBrowse 2 | JBrowse 1 |
| ------------------------------------------------------------------- | ----------------------- | ------------------ |
| Status updates during track loading (e.g. Downloading BAM index...) | :heavy_check_mark: | :x: |
| Uses webworkers for parsing and rendering tracks | :heavy_check_mark: | :x: |
| Supports interactive editing of configuration in the app | :heavy_check_mark: | :x: |
| Can "flip" or reverse complement the linear view | :heavy_check_mark: | :x: |
| Hi-C data rendering | :heavy_check_mark: | :x: |
| Can display multiple chromosomes in a single view | :heavy_check_mark: | :x: |
| Sort read pileup in alignments tracks | :heavy_check_mark: | :x: |
| Show soft clipping in alignments tracks | :heavy_check_mark: | :x: |
| Built-in spreadsheet-like view for datasets | :heavy_check_mark: | :x: |
| Can connect to UCSC track hubs | :heavy_check_mark: [^1] | :x: |
| Can load plugins at run-time instead of build time | :heavy_check_mark: [^2] | :x: |
| Non-admin users can open tracks and share them with others | :heavy_check_mark: [^3] | :x: |
| Re-usable NPM package | :heavy_check_mark: [^3] | :x: |
| Name searching e.g. ability to type a gene name/ID to search for it | :x: | :heavy_check_mark: |
| URL query params API e.g. specifying ?loc=chr1:1-100 in URL bar | :x: | :heavy_check_mark: |

[^1] Requires that the trackhub host support CORS for the jbrowse-web, jbrowse-desktop does not require this however

Expand All @@ -74,3 +77,20 @@ Here is a short list of current data format support
- Indexed FASTA/BGZip indexed FASTA
- 2bit
- .hic (Hi-C contact matrix visualization)

## Embeddability

JBrowse 1 has some notion of being embeddable but it is not ideal and it
doesn't have very optimal routes for being packaged and re-used on NPM

With JBrowse 2 we have some new concepts for embeddability. For example, we can
install just the linear-genome-view and use it as a react component.

The @jbrowse/react-linear-genome-view is specialized for certain use cases and
is not hooked up to session sharing, URL params, or anything but instead is a
simple React component

See here for more details https://www.npmjs.com/package/@jbrowse/react-linear-genome-view

Note that the entire jbrowse-web app that contains multiple views can't
currently be installed via NPM though