Optimized genome browser

Question

[Rogerio Ribeiro]

Hello Biostars comunity,

For my project, I'm working with the transcriptome of a non-model organism, which has an incomplete and in many cases incorrect reference annotation. As such, I have to manually inspect the gene models, and compare them with assembled transcripts, long reads alignment, etc. I've using Jbrowser for the last 2 months, however, this software crashes every time I try to change scaffold or even if I load 4 or 5 tracks. This makes my job much less productive.

Does anyone have experience with this kind of problem, and as found a workaround, solution? (i.e using another more optimized genome browser?).

Best

[cmdcolin]

Hi there, I'm a jbrowse dev. If you are interested feel free to send me an email [e-mail] I can check out what you're looking at...definitely would be interested to help :)

Answer 1

[GenoMax]

Artemis (LINK) may be one option. What you are looking for is an annotation tool in addition to a genome browser. There are plenty of genome browsers but not many with annotation tools.

[Rogerio Ribeiro]

For genome annotation tool I'm currently working with MIKADO to refine my transcriptome assembly. However, I want to be able to inspect some results and visualize my candidate genes. I'll check Artemis for visualization.

Answer 2

[cmdcolin]

In a follow up email to the OP we found that what was needed was to load tabix indexed GFF instead of plain GFF

The unindexed GFF caused slowness on scaffold switches

To create indexed GFF my general strategy is

sudo apt install genometools
gt gff3 -sortlines -tidy -retainids source.gff > source.sorted.gff
bgzip source.sorted.gff
tabix source.sorted.gff.gz

Then loading source.sorted.gff.gz and the tabix index for it into jbrowse helps

Answer 3

[lieven.sterck]

GenomeView might be an other option worth investigating . It does both browsing, visualization as well as a gene editing tool