SRA Explorer

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

You have {{ savedResults.length }} 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
{{ x.title }} {{ x.accession }} {{ x.platform }} {{ x.total_bases }} {{ x.createdate | date:'dd MMM yyyy' }}

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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{{ x.fastq_url }}{{ nlChr }}

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{{ nlChr }}curl -L {{ x.fastq_url }} -o {{ x.fastq_niceFilename }}

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{{ nlChr }}ascp -QT -l 300m -P33001 -i {{ ascp_openssh_location }} {{ x.fastq_asperaurl }} . && mv {{ x.fastq_filename }} {{ x.fastq_niceFilename }}

This list of URLs is followed by a nicer filename, with the cleaned dataset title appended. This is suitable for use with the Cluster Flow --file_list download option.

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{{ x.fastq_url }}{{ tabChr }}{{ x.fastq_niceFilename }}{{ nlChr }}

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{{ nlChr }}{{ x.fastq_url }},{{ x.fastq_niceFilename }}


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.

{{ x.sra_url }}{{ nlChr }}

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{{ nlChr }}curl -L {{ x.sra_url }} -o {{ x.sra_niceFilename }}

This list of URLs is followed by a nicer filename, with the cleaned dataset title appended. This is suitable for use with the Cluster Flow --file_list download option. 

{{ x.sra_url }}{{ tabChr }}{{ x.sra_niceFilename }}{{ nlChr }}


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{{ tabChr }}Title{{ tabChr }}Platform{{ tabChr }}Total bases{{ tabChr }}Create date{{ tabChr }}SRA URL{{ tabChr }}SRA filename{{ tabChr }}SRA nice filename{{ tabChr }}FastQ URL{{ tabChr }}FastQ Aspera URL{{ tabChr }}FastQ filename{{ tabChr }}FastQ nice filename{{ nlChr }}{{ x.accession }}{{ tabChr }}{{ x.title }}{{ tabChr }}{{ x.platform }}{{ tabChr }}{{ x.total_bases }}{{ tabChr }}{{ x.createdate }}{{ tabChr }}{{ x.sra_url }}{{ tabChr }}{{ x.accession }}.sra{{ tabChr }}{{ x.sra_niceFilename }}{{ tabChr }}{{ x.fastq_url }}{{ tabChr }}{{ x.fastq_asperaurl }}{{ tabChr }}{{ x.fastq_filename }}{{ tabChr }}{{ x.fastq_niceFilename }}

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

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{{ savedResultsENAfastq | json }}

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

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{{ savedResultsENAfastqYAML }}

Query URL =