Genome Annotation Python Packages

aegis-bio

Annotation Extraction Genomic Integration Suite (AEGIS) is a powerful and flexible Python-based suite for the manipulation, analysis, and integration of genomic annotations. It is based on a robust object-orientated framework. Available in PyPI, Docker Hub and as a Github container in GHRC.

kegganog

🤝 Tool for mining KEGG pathways completeness data from eggNOG-mapper annotations

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

edge-genome

Genome Engineering Tool

tigre

TIGRE is a Python CLI for large scale extraction of intergenic regions.

plastburstalign

A Python tool to extract and align genes, introns, and intergenic spacers across thousands of plastid genomes using associative arrays

lifton

🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

bricks2marble

Pre- and postprocessing tools for genome annotation.

peaks2utr

A robust, parallelized Python CLI for annotating three_prime_UTR

funannotate

funannotate: eukaryotic genome annotation pipeline

ga4gh

A reference implementation of the GA4GH API

gdt

Gene Dictionary Tool - Bioinformatics package

gffbase

GFFBase — Rust+DuckDB GFF3/GTF engine

txdb

Access TxDB Annotation objects

sismis

Secretion system discovery tool.

gffy

Fast, low-RAM GFF3/GTF tools: annotrieve-compatible stats, bulk JSONL, GTF-to-GFF3 conversion; large files sorted by seqid (GNU sort) then streamed per-chromosome

orgdb

Access OrgDB annotations

ga4gh-server

A reference implementation of the GA4GH API