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.

Query the ENA for different types of data and bulk download

test

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.

Dresser-un-fonctionnaire.com

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

Python CLI for querying and downloading RNA-Seq metadata from the EMBL-EBI ENA Portal by NCBI taxonomy ID. Supports tax_tree expansion, streaming TSV/JSON output, and robust retry/backoff for reliable large-scale transcriptomic data retrieval.

Source codes of API queries in R (made available together with datasets) of Medical Translation in the History of Modern Genomics (TRANSGENE)