SRA Explorer

This tool aims to make datasets within the Sequence Read Archive more accessible.

You have 0 datasets in your collection. View saved datasets.

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Select relevant datasets and click add to collection. When you're finished, view all saved datasets with the button in the top right of the page, where you can copy the SRA URLs.

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Title Accession Instrument Total Bases (Mb) Date Created

0 Saved Datasets


To download FastQ files directly, sra-explorer queries the ENA for each SRA run accession number.

The following is a list of links to download the selected SRA runs as FastQ from the ENA.

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This list of bash curl commands to download each SRA run FastQ file from the ENA, and save with a nicer filename, with the cleaned dataset title appended.

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#!/usr/bin/env bash

This list of bash ascp commands to download each FastQ file from the ENA using the Aspera download tool.

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#!/usr/bin/env bash

This list of URLs is followed by a nicer filename. This is suitable for use with bcbio-nextgen analysis pipelines.

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samplename,description


These download links are automatically generated based on the URL schema of the NCBI SRA.

The following is a list of links to download the selected SRA files.

This list of bash curl commands to download each SRA file and save with a nicer filename, with the cleaned dataset title appended.

#!/usr/bin/env bash


These files contain the metadata used by SRA-Explorer for downstream use. Note that each SRA record is repeated for every ENA FastQ entry.

The following is a TSV (tab separated values) file with all metadata fields for the selected samples.

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Accession	Title	Platform	Total bases	Create date	SRA URL	SRA filename	SRA nice filename	FastQ URL	FastQ Aspera URL	FastQ filename	FastQ nice filename

The following is a JSON file with all metadata fields for the selected samples.

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[]

The following is a YAML file with all metadata fields for the selected samples.

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Nextflow and the Seqera Platform enable scalable and reproducible scientific workflows. Many Nextflow pipelines use a sample sheet .csv file to handle input metadata. This can be supplied within Seqera Platform as a Dataset. SRA-Explorer allows metadata from public sequencing data to be saved as a Dataset in Seqera Platform.

Note that SRA records are repeated for every ENA FastQ entry.

Send all metadata to Seqera Platform as a saved Dataset, which you can use as an input when launching pipelines.

Please connect your Seqera Platform account to proceed.

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Accession Title Platform Total bases Create date SRA URL SRA filename SRA nice filename FastQ URL FastQ Aspera URL FastQ filename FastQ nice filename

Query URL = 0

SRA-Explorer was written by Phil Ewels. Source code is available under a GNU GPLv3 licence at https://github.com/ewels/sra-explorer.

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