This tool aims to make datasets within the Sequence Read Archive more accessible.SRA-Explorer allows you to collect SRA datasets and get a quick bash download script for either SRA files or now FastQ files! (courtesy of the ENA API)
It doesn't have any extra functionality though, just finding URLs basically. If the ENA has a consistent FTL URL structure then it should be simple to extend it to work with direct FastQ downloads too though.
enaBrowserTools
A collection of scripts to assist in the retrieval of data from the ENA Browser
pysradb
Package for fetching metadata and downloading data from SRA
Choudhary S. pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive [version 1; peer review: awaiting peer review]. F1000Research 2019, 8:532 (https://doi.org/10.12688/f1000research.18676.1)
Downloading published fastq data from GEO
This guide will show you how to download fastq format data from published papers.
This tool aims to make datasets within the Sequence Read Archive more accessible.SRA-Explorer allows you to collect SRA datasets and get a quick bash download script for either SRA files or now FastQ files! (courtesy of the ENA API)
https://github.com/ewels/sra-explorer
It doesn't have any extra functionality though, just finding URLs basically. If the ENA has a consistent FTL URL structure then it should be simple to extend it to work with direct FastQ downloads too though.
A collection of scripts to assist in the retrieval of data from the ENA Browser
Package for fetching metadata and downloading data from SRA
Choudhary S. pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive [version 1; peer review: awaiting peer review]. F1000Research 2019, 8:532 (https://doi.org/10.12688/f1000research.18676.1)
This guide will show you how to download fastq format data from published papers.
Look in the paper for the GEO accession number and then go to the GEO website: http://www.ncbi.nlm.nih.gov/geo/
Enter the GEO accession code for that data you want to download (e.g. GSE37757) and click Search
https://www.cbrg.ox.ac.uk/cbrg/docs/downloading_fastq_GEO.pdf
R Interface to the NCBI SRA metadata https://seandavi.github.io/SRAdbV2/