GGA is a group of projects focused on supporting genome annotation inside Galaxy.
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)
A production ready Docker image for Tripal v2.x and v3.x.
A production ready Docker image for JBrowse.
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.
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 library for talking to Apollo API. This includes the experimental
Arrow Apollo client.
A Python library for interacting with Tripal
A Python library for interacting with Chado database
Galaxy tools for Genome Annotation.
Convenient wrapper around Circos allowing building of a huge variety of highly configurable Circos plots. This will eventually be merged into the IUC repository.
Backup an apollo instance to a git repository
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.
This material is based upon work supported by the National Science Foundation under Grant Number (Award 1565146)