⚡ ♒ Rapid prokaryotic genome annotation

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Extensive de-novo TE Annotator

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Eukaryotic Genome Annotation Pipeline

Genomic Data Retrieval with R

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Earl Grey: A fully automated TE curation and annotation pipeline

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

convert various features into a GFF-like file for use in genome browsers

Read Assembly and Annotation Pipeline Tool

A fully automated gene annotator from RNA-Seq expression data

Tools to annotate genomes using long read transcriptomics data

A parallel wrapper for LTR_FINDER

A set of workflows written in Nextflow for Genome Annotation.

Genome Annotation Without Nightmares

Efficiently keep track of changes to genomes

Example client programs for Saphetor's VarSome annotation API