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

Collecting Genotypes from ENA and make their SNPs

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

Mirror selected ENA data locally

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

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

血小板转录组fastq数据处理

test

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

Query the ENA for different types of data and bulk download

Dresser-un-fonctionnaire.com

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