Colin Diesh

Render translated proteins on gene glyphs themselves

1

This is a feature of both IGV and UCSC. Without this feature, users have to look up the 3frame translation on the DNA sequence track in the right coding frame...

Create BEDPE parser

2

BEDPE data is a simple format that shows interactions between two regions of the genome, and sometimes breakend data can come in this format Small data files could be parsed...

Currently the theme is a cool concept, but is not easily editable via any config editor (and I believe it is sort of a random json blob so not really...

Add a feature to zoom in on the ends of a large structural variant using discontinuous display regions

1

With a large SV, it could be useful to create two displayedRegions zooming on on the ends of the SV event, so that you can look at the coverage drop-offs...

step 1. visit https://jbrowse.org/demos/cgv-cra5/ step 2. press ctrl+t to open a new tab step 3. wait, and then click back to the cgv demo The circular view ends up being...

After floating labels merge #2781 , the horizontally flipped mode can have some label collisions To properly do the layout, the layout should basically be done in the reverse orientation...

T2T genome for quickstart on desktop

1

add synteny to hg38 and reference gene track if possible too

Linear synteny multi-way comparisons

2

The current linear synteny code is very pairwise oriented. It needs enhancement to handle multi-way comparisons. This can be a series of pairwise comparisons (stack) but possibly over multiple windows

Possible slowness turning on and off tracks in synteny view

2

This was just somewhat unexpected but toggling a track can be slow, maybe with the linear synteny view particularly Example: Visit https://jbrowse.org/code/jb2/v1.6.5/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-kY4TSOUAUD&password=wHcxI Then turn off or on the synteny track...