Comments (1)
meren
commented on July 26, 2024
Dear Quentin,
This tool has been very useful for us to study the conservancy of gene clusters or functions in synteny across genomes, but it doesn't offer a lot of downstream visualization options in anvi'o. Your output shows the gene clusters that occur next to one another across genomes. More information is here: https://anvio.org/help/main/programs/anvi-analyze-synteny/
We are now developing a new strategy, but it will need another few months to be ready for prime time.
Best wishes,
from anvio.
Related Issues (20)
- [BUG] pulp v2.8 made API changes that cause errors generating workflow DAG diagrams HOT 1
- [BUG] Can't create phylogenomic tree, as phylogenomic-tree.txt and default collection has different number of items.
- [BUG] Can't create phylogenomic tree, as phylogenomic-tree.txt and default collection has different number of items. HOT 3
- [BUG] Can't visualise the pangenome with average nucleotide identity HOT 1
- [BUG] anvi-setup-scgs-taxonomy STILL writes SCGs database to default location HOT 2
- [FEATURE REQUEST] add parameter --temp for temporary files path HOT 5
- [FEATURE REQUEST] Refactoring Anvio to be more eukaryote friendly/account for different genetic architectures
- [FEATURE REQUEST] Different gene caller option(s) for `anvi-gen-contigs-database` HOT 5
- [FEATURE REQUEST] See external/third-party dependencies on program documentation pages HOT 1
- [FEATURE REQUEST] Adding a program to annotate viral PHROGs via their HMMs
- [FEATURE REQUEST] A shortcut for importing layer orders that doesn't go through `anvi-import-misc-data`
- [FEATURE REQUEST] Environment variables for KEGG, Pfam, and other data directories so sys admins can set a global --xxxx-data-dir value
- [FEATURE REQUEST] Annotate which KOfams were added by our bitscore relaxation heuristic
- [FEATURE REQUEST] A conda package for anvi'o with a minimal installation option
- [BUG] `--prodigal-single-mode` breaks metagenomic workflow HOT 5
- [BUG] anvio-cluster-contigs fails with Generate input data
- [BUG] anvi-meta-pan-genome does not allow me to use gene calls not from prodigal HOT 10
- [BUG] Missing USearch in installation instruction and workflow DAG declarations HOT 1
- [BUG] contigs.db has issues when inputing aa_sequence in the external-gene-call file HOT 4
- [BUG] MaxBin2 failing due to one missing coverage 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 anvio.