Comments (2)
Hi Federico @FedeGueli!
Yes, that's been on our radar for some time, but we never had enough time to work on it.
We've been also receiving conflicting requests. Some people want more info columns and less space for the sequence view, or even to completely remove it. Others are only interested in sequence view and want to remove the extra columns to give some more space for it. There's been also a pressure on us to not add any more extra columns, even if we considered the new info potentially useful. I guess it depends on individual use case and in the end the table should be configurable somehow.
As a workaroung, you can download the alignment and/or translation fasta and inspect them in alignment viewer of your choice (e.g. AliView is not bad). I realize that it's not as convenient though.
The upcoming Nextclade v3 (here is an early, potentially buggy preview of it) groups aa mutations that are not only immediately adjacent but also 1-codon away. This makes slightly less groups and they are slightly more compact in the sequence view. Perhaps this can help a little? But I realize it's not the final solution either.
Ideally, want a fully-featured alignment viewer, with pan & zoom, so that you can scale and scroll the view and, perhaps, if you zoom close enough even see individual nucs/aas. But it's quite challenging to implement in a web app, and, especially, embed it into the existing table rows. So I cannot give any promises here. We are a small research lab and have to balance our time between different things.
You can help to make it happen: if you or someone you know have dev skills and time to implement this feature, consider contributing to the project - it's open source.
Related:
from nextclade.
Thank you very much Ivan, i ve tried the V3 and it resolves all my requests!! Thank you very much!!
You as a little team did a huge work a a huge thanks is deserved to you.
Without your work any fast efficient variant spotting and tracking would have been delayed a lot.
Unfortunately no coding here ! But happy to help in any other way (test, feedback, whatever) .
ah maybe variant spotters with coding skills as @aviczhl2 @Over-There-Is @olias120676 could have some time to help.
Thank you very much!
from nextclade.
Related Issues (20)
- Incorporation of enterovirus dataset into nextalde docker container HOT 1
- Include aligned sequences and translations in ndjson
- ENH(nextalign cli): show default values in --help usage statement HOT 4
- Maximum Sequence Limit? HOT 2
- Web: Grey scale coloring for region/country/divison if scale not predefined in reference tree HOT 5
- How to decide if the reversionSubstitutions are valid variants or not and whether to keep them? HOT 2
- Direct Auspice SVG Download
- Updating certain parts of the JSON file output from Map to Array HOT 2
- linux-musl artefact gets slower rather than faster when parallelizing in contrast to gnu HOT 5
- Parsing PCR primers HOT 1
- how many SARS-COV-2 sequences can nextclade handle in a MSA file? HOT 8
- Is there any example for handling HIV data? HOT 2
- Web crash: The target <seqName> could not be identified in the dom HOT 2
- Show "browser not supported HOT 1
- Show "browser not supported" modal only once per session HOT 3
- if the qc.overallStatus of my sequences are mediocre, can we keep them for next step analysis? HOT 5
- web-based nextclade issue when using another reference HOT 8
- web(minor): when customizing dataset files, it always says "pasted sequences" even if the field is for tree HOT 2
- I upload 1490 sequences to nextclade, and upload to auspice.us, why it shows me 4255 sequences? HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from nextclade.