Genome Browser suggestions

Question

[Matteo Schiavinato]

Hi all,

I am in search of a Genome Browser that could suit my needs. I already used many times GBrowse, IGV and Jbrowse. GBrowse is too tedious to work with given the way you have to add tracks and given that is very slow when the database becomes big. JBrowse is awesome but doesn't feature an SVG export as GBrowse instead does. IGV is nice but the image export sucks in quality. What I'm searching for now is a GB that:

1. Is faster than GBrowse
2. Can export SVG images
3. Has a nice layout that suits publication-level images (i need many of them)
4. EDIT: supports reference genome upload from files

Do you guys have any suggestion? Please don't suggest anything that doesn't fulfill all of these 3 criteria: I probably have already tried it out and discarded it :D

Thanks!

[GenoMax]

See: A: Portable genome browser

[ATpoint]

May I ask what problems you had with IGVs quality? Did you export as SVG?

[Matteo Schiavinato]

The version I have of it doesn't support it. In case modern versions do, then I would upgrade it.

[ATpoint]

2.3.79 does support png, svg and jpeg.

[GenoMax]

What version are you using? I thought IGV always had SVG export. IGV is currently v. 2.3.97.

[Matteo Schiavinato]

Fixed. I am using IGV with sVG export now. The thing was: we had IGV on a node which was usually logged in to without -X, and could for some reason render png but not svg (don't ask me why, perhaps some graphic libraries not loaded). Now it exports nice SVGs!

Answer 1

[cmdcolin]

We have been developing JBrowse 2, a genome browser with a bunch of different visualization modalities including linear, circular, etc. Currently linear views have SVG exports. The app can be deployed on the web e.g. for model organism databases or installed as an app for desktop use

The SVG exports are also stripped of excessive UI so look fairly clean

You can also automate the generation of static SVG images using our command line tool https://www.npmjs.com/package/@jbrowse/img

More pictures here https://jbrowse.org/jb2/gallery/

[Istvan Albert]

You should make a separate post of a NEWS type. I knew of JBrowse but not of version 2.0 which is now a standalone app.

[cmdcolin]

thanks, would be happy to :) I will try to draft up a post soon!

Answer 2

[Charles Plessy]

How about ZENBU ?

Here is an example illustration that I made starting from ZENBU's SVG export.

[Matteo Schiavinato]

Thank you, this looks nice. Can I load my reference genome? Because I don't work with a canonical organism.

[Charles Plessy]

It's work in progress. At the moment you would need to contact the browser admin.

Answer 3

[Alex Reynolds]

UCSC Genome Browser + soda.py for automated PDF figure generation.

Answer 4

[dariober]

Full disclosure: I'm the author of it. I wonder if ASCIIGenome is any use to you?

It has a different approach from the other browsers as it is controlled via the command line, either interactively or automated (with some optimism I like to think of it as the vim of genome browsers). It displays genomic data directly to the terminal screen, as such it is easy to automate and since you say you have lots of images to print it may help.

It can save pictures in text or pdf format so figure quality is not an issue, but of course, it deliberately doesn't have the fancy layout of IGV and similar. The reference genome can be loaded from fasta file.

Here's an example in non-interactive mode:

ASCIIGenome -ni -x 'save test.pdf' ds051.actb.bam

The pdf figure looks like

[Matteo Schiavinato]

I doesn't go in the direction of what I need but it's fancy and super cool, I think I will try it out for my personal purposes! :)

[dariober]

Thanks for your comment - Feel free to drop an issue on github or a post here on biostars if you have any questions.

[GenoMax]

Does ASCIIGenome support navigation using the arrow keys?

[dariober]

Hi- There are a few options to navigate but they don't use the arrow keys (!). The UP and DOWN keys scroll commands like in most terminal shells. To move left and right one can use keys f and b (forward/backwards) or +10k and -10k to move 10kb forward or backwards. More on navigation here.

Unfortunately, I must admit the navigation is not as smooth as in samtools tview since between one execution of a movement and the next there is a bit of delay (sort of similar to IGV I guess).

[GenoMax]

Would be useful if you can support <- and -> arrow keys along with with some additional combination (ctrl + arrow etc to allow longer jumps 100kb etc)? I tend to use the arrow keys for navigation on the command line and they feel like a natural extension of what is happening on the display.

Is there a specific reason for requiring a return after pressing f/b keys? I noticed that subsequent simple returns are used to repeat the last f/b directive. Perhaps that is the reason?

[dariober]

Thanks for comments! Of course, I see what you mean about arrow keys being more intuitive. The reason for "return" after a command is to send the input string to ASCIIGenome which then it interprets it as appropriate, just like you need ls followed by <ENTER> at the Bash terminal. A subsequent ENTER will repeat the previous command, whatever that was. It may be possible to map the left and right keys to some behavior like f/b, but I'm not sure...

About long jumps, it's a bit tricky to define a "good" behavior since, for example, 100kb may be a big jump in some cases but a small jump in others. For this, f/b move by default 1/10 of the current genomic window, which roughly is a small jump. However, you can pass a number to f/b to make the window move by a proportion of the genomic window, e.g. f 0.5 moves forward 1/2 of the current window (and this is the same as the ff/bb commands). Then of course, for jumps of a defined size you can use +/-INT as I mentioned above.

[GenoMax]

It may be possible to map the left and right keys to some behavior like f/b

That would be great. It would allow one to scroll left/right seamlessly without having to hit the keyboard for f/b. Is the screen jump/move interval configurable?

Answer 5

[simon.vanheeringen]

Why not use the UCSC Genome Browser? You can add tracks using track hubs and support non-standard genomes using assembly hubs, see here: https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html. The advantage of track hubs is that you only have to create them once, and then you can use always use your tracks, configured as you like them. No SVG export, but there is PDF export which is easily converted.

[Matteo Schiavinato]

UCSC Genome Browser is waaaaaay too slow for my needs (I tried).

[genecats.ucsc]

Was there anything in particular that was too slow? I can create a bug report for it if there was something specific.

Thanks, ChrisL from the UCSC Genome Browser

[Matteo Schiavinato]

I don't think it's a problem of UCSC Genome Browser itself, but more of its interaction with our system. We basically have to find one that works fine with our set-up (I am not the sysadmin so I can't go further in details here, I would go out of my league).

Answer 6

[Joe]

I almost exclusively use ARTEMIS