GGA

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Galaxy Genome Annotation

View the Project on GitHub galaxy-genome-annotation/galaxy-genome-annotation.github.io

Galaxy Genome Annotation

GGA is a group of projects focused on supporting genome annotation inside Galaxy, in particular:

Galaxy tools

Analysis tools

License

Various Galaxy tools for Genome Annotation are in the IUC repository, including: Augustus, BUSCO, FeelNC, Funannotate, Gffread, InterProScan, Maker, Metaeuk, Prokka, Repeat Masker, Repeat Modeler, Snap

Other tools are also available on other repositories: Antismash, Braker, EggNOG-Mapper

Visualisation tools

License

We are maintaining the following Galaxy tools for the visualisation of annotations:

Circo in Galaxy

JBrowse in Galaxy

Galaxy tools for GMOD apps

GitHub Contributors License

Galaxy tools to interact with GMOD applications (see below for the corresponding Docker images and Python libraries).

Training Material

Learn how to annotate new genomes by following the Genome Annotation tutorials on the Galaxy Training Network! Reusable workflows are provided together with detailed tutorials and videos.

Apollo tooling and service

Apollo server at UseGalaxy.eu

Based on the various components listed here, UseGalaxy.eu is hosting an Apollo server, freely accessible to the community.

Apollo in Galaxy

Using Galaxy, any user can upload its own organism, and start curating gene models collaboratively with other users.

Check out the GTN training material to learn how to use it!

Permapol

GitHub Contributors License

Permapol is a permission manager for Apollo, designed to ease collaboration when coupled with a Galaxy instance.

Apolpi

GitHub Contributors License

Apolpi is a tiny Flask application reimplementing a specific API function (organism listing) of Apollo, to make it run way faster.

Apollo report

GitHub Contributors License

Apollo report is a Docker image that contains everything needed to generate an Apollo per-user report each day. Based on the validation rules defined at http://bipaa.genouest.org/.

Docker images

docker-galaxy-genome-annotation

GitHub Contributors License

Galaxy Docker repository with tools for Genome Annotation. The image is built with tools for Assembly (Spades, Mira), Structural Prediction (Glimmer, Augustus), Functional Prediction (BLAST+, InterProScan, BLAST, Diamond, Blast2GO), various Utilities (FASTA manipulation tools, EMBOSS), tools for Comparative Genomics (CD-Hit, ClustalW, AntiSmash, mummer), and finally Annotation & Visualization tools (Apollo Tools, JBrowse-in-Galaxy, JBrowse-in-Galaxy Extras, Tripal Admin tools, Circos)

docker-tripal

GitHub Contributors License

A production ready Docker image for Tripal v2.x and v3.x.

docker-jbrowse

GitHub Contributors License

A production ready Docker image for JBrowse.

docker-chado

GitHub Contributors License

A production ready Docker image for Chado database. The image is built automatically using SQL dumps produced by chado-schema-builder, including up-to-date ontologies.

dockerized-gmod-deployment

GitHub Contributors License

If customizing the docker-galaxy-genome-annotation image isn’t your style, this is a preconfigured deployment of Galaxy + Apollo + Chado + Tripal + JBrowse + JBrowse REST API + PostGraphQL + JBrowse GraphQL Experiment all as a docker-compose.yml

Python libraries

python-apollo

GitHub Contributors License

Python library for talking to Apollo API. This includes the experimental Arrow Apollo client.

python-tripal

GitHub Contributors License

A Python library for interacting with Tripal

python-chado

GitHub Contributors License

A Python library for interacting with Chado database

Experiments

apollo-git-backup

GitHub Contributors License

Backup an apollo instance to a git repository

apollo-google-docs-integration

GitHub Contributors License

Experimental work for a plugin to allow referencing data from Apollo. For genomes which are re-opened / re-numbered / etc. between drafting and publication, it can be extremely helpful to reference persistent identifiers.

Support

This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146) and with the support of the Erasmus+ programme of the European Union (2020-1-NL01-KA203-064717).

This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union.