Package for fetching metadata and downloading data from SRA/ENA/GEO

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

Prepares a SARS-CoV-2 submission for GISAID, NCBI or ENA. Can read GISAID or NCBI files, or plain fasta+tsv/csv/xls. Finds files in input directory and merges everything into a single output directory. Auto-detects input file formats. Can submit the results to multiple repositories from the command line.

A Python library for interacting with ENA's API

TSV and XLSX templates for submitting ENA objects (study, experiment, sample and run) using the ENA-upload-tool

OMD Curation Toolkit is a python package designed for the download and curation of metadata and fastq files of public omics datasets.

Collecting Genotypes from ENA and make their SNPs

Snakemake workflow to upload Sars-Cov-2 reads to ENA

Mirror selected ENA data locally

Query the ENA for different types of data and bulk download

Windows desktop app for downloading ENA FASTQ and GEO supplementary files.

Command-line tool for fast, automated downloading of raw FASTQ files from ENA and/or GEO, supporting variety of NGS datasets, including bulk and single-cell RNA-seq.

FAIRy rulepacks for ENA/SRA: validate submission metadata + read/QC manifests early, with actionable “how to fix” guidance.

Epistemic Network Analysis in pure Python — a port of the R package rENA, verified numerically against it. The project started from July 2025. pip install ena-python

Python CLI for querying and downloading RNA-Seq metadata from the EMBL-EBI ENA Portal by NCBI taxonomy ID.

Tracks downstream reuse of plant DNA sequences across scientific literature and patents — a DSI traceability tool built on ENA, NCBI, and EuropePMC APIs.

Python wrappers for RF lab instruments — Mini-Circuits USB power sensors and Agilent E5061B ENA — with FastAPI servers for n8n and a live Smith chart viewer.