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.

3K 15 1

gffbase

🧬 GFFBase — Rust+DuckDB GFF3/GTF engine

3K 11 5

lifton

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

2K 132 18

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

2K 683 87

kegganog

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

956 43 4

edge-genome

Efficiently keep track of changes to genomes

858 38 4

bricks2marble

Pre- and postprocessing tools for genome annotation.

806 4 0

peaks2utr

A robust Python tool for the annotation of 3’ UTRs

695 25 3

plastburstalign

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

543 1 1

txdb

Access TxDB Annotation objects

471 2 0

pybarrnap

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

351 29 1

phagemine

Phage-focused genome annotation and comparative genomics workflow integrating structural gene prediction, evidence-supported functional annotation, and INPHARED nearest-phage analysis.

340 2 0

funannotate

Eukaryotic Genome Annotation Pipeline

308 401 95

tigre

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

301 3 0

ga4gh

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

295 98 91

gdt

GDT is a tool for gene dictionary management, works with annotated genomes, handles .gdict and GFF3 files, and provides both programmatic and interactive interface.

235 4 0

ploidypatch

Duplication-aware, review-first plant gene-model repair with auditable and reversible GFF3 patches

136 0 0

sismis

Machine learning-based secretion system annotation tool

81 3 0

gffy

gffy — A fast GFF statistics extractor. Well, because the world needed another one.

67 3 1

orgdb

Access OrgDb Annotation objects

56 1 0

ga4gh-server

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

41 98 91