ena

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

Pipeline to fetch metadata and raw FastQ files from public databases

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

R functions and workflow for submitting amplicon sequence data to the ENA.

Packer templates for building OpenBSD cloud machine images (AWS/GCP)

Query the ENA for different types of data and bulk download

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

Create, edit, and validate scientific metadata against a standard (MIAPPE, ISA, Darwin Core, DiSSCo, ENA, PRIDE, MetaboLights, FAIRDOM-SEEK) from a YAML profile — CLI, web interface, Python API, and MCP server.

test

Self-hosted web platform for sequencing facilities: orders, samples, MIxS metadata, sequencing files, bioinformatics pipelines, and ENA submission.

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.

Codex skill for resolving and downloading public GEO, NCBI, and ENA data with IBM Aspera ascp