paper.md

title	tags	authors	affiliations	date	bibliography
fastq-dl: efficiently download sequences from ENA and SRA	fastq download python bioinformatics	name orcid affiliation Robert A. Petit III 0000-0002-1350-9426 1, 2 name orcid affiliation Michael B. Hall 0000-0003-3683-6208 3 name orcid affiliation Gerry Tonkin-Hill 0000-0002-1350-9426 4 name affiliation Jie Zhu 5 name orcid affiliation Timothy D. Read 0000-0001-8966-9680 2	name index Wyoming Public Health Laboratory, Wyoming Department of Health, Cheyenne, Wyoming, USA 1 name index Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA 2 name index Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia 3 name index Department of Biostatistics, University of Oslo, Oslo, Norway 4 name index Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China 5	17 June 2023	paper.bib

Summary

fastq-dl is a convenient bioinformatic tool that simplifies the process of retrieving FASTQ files from ENA and SRA. It was developed to be easy to use and accessible to researchers from all backgrounds. By facilitating efficient downloading of publicly available FASTQ files, users can easily integrate these data into their own research. fastq-dl is available from PyPI and Bioconda for simple installation, and the source code is available at https://github.com/rpetit3/fastq-dl.

Statement of Need

High-throughput sequencing technologies have revolutionized the field of genomics, enabling researchers to generate vast amounts of data quickly and at relatively low cost. The European Nucleotide Archive (ENA) [@Burgin_2023] and the Sequence Read Archive (SRA) [@Katz_2022] are two major repositories for publicly hosting next-generation sequencing data from many research projects. Retrieving sequences from these repositories is often a multi-step process and difficult for researchers who lack experience with bioinformatics. fastq-dl is a bioinformatic tool that simplifies this process of downloading sequences from SRA and ENA.

Implementation

fastq-dl is written in Python and is designed to be user-friendly and simple to use. Users can submit queries to the ENA, via a REST API [@Burgin_2023], or SRA, via pysradb [@Choudhary_2019], with fallback mechanisms in the event either repository is down. fastq-dl supports a range of query types, including taxon ids, species names, and accessions, including BioSample, BioProject, Experiment, and Run Accessions. A query will return metadata for each hit and save this metadata to a tab-delimited file. Unless disabled by the user, fastq-dl will then proceed to download available sequences for each hit of the query. If using ENA, raw FASTQs are downloaded using their available FTP service, otherwise fasterq-dump [@Katz_2022] is used to download from SRA. In the event a repository is unresponsive, download attempts will be made against the other repository. When an Experiment or BioSample has multiple Run accessions associated with it, users can optionally choose to merge these Run accessions. Upon completion, users are provided with a summary file, a metadata file and FASTQ files per-query hit.

Funding

This project was partially supported by the Georgia Emerging Infections Program and the Wyoming Department of Health

References