Gff3 Python Packages

pygenomeviz

A genome visualization python package for comparative genomics

filterx

process any file in tabular format. Fasta/fastq/GTF/GFF/VCF/SAM/BED

tigre

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

gff3tool

Python programs for processing GFF3 files

bioino

💻 Interconverting FASTA, GFF, and CSV.

gdt

Gene Dictionary Tool - Bioinformatics package

genome-format-converters

A unified Python CLI for 30 bioinformatics file-format conversions (VCF, GFF3, GTF, BED, GenBank, FASTA, FASTQ, BAM, EIGENSTRAT, PLINK, MAF, MUMmer, HMMER, Newick) with consistent flags, batch mode, and a published Stage 1 benchmark vs convertf, plink2, AGAT, gffread, UCSC, EMBOSS, pyhmmer.

divbrowse

A web application for interactive visualization and exploratory data analysis of variant call matrices

gff-toolkit

Tools for handling gff files

vcfsynonymous

Detect synonymous genetic variants in VCF

gff2parquet

Utility CLI for handling GFF files (incl. converting to parquet)

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

gbgb

Goodbye, GenBank is a package for use with Biopython that gives feature annotations from GenBank records a new and better life.