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

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

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

Query the ENA for different types of data and bulk download

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

Helps research teams create, validate and share standardized metadata: MIAPPE, ISA, Darwin Core, DiSSCo and the ENA, PRIDE and MetaboLights formats as guided forms with automated checks and vocabulary suggestions; import public records, export for repositories, compare or combine standards. Browser, CLI, Python or AI assistant.

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.

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