Top 11 genome-annotation open source projects

Example client programs for Saphetor's VarSome annotation API

Earl Grey: A fully automated TE curation and annotation pipeline

Toolkit for preparing genomes for submission to NCBI

A parallel wrapper for LTR_FINDER

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.

Extensive de-novo TE Annotator

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Pipeline for annotating genomes using long read transcriptomics data with pinfish

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Genome Annotation Without Nightmares