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.

Select relevant datasets and click add to collection. When you're finished, view all saved datasets with the button over the "Add to collection" button, where you can copy the SRA URLs.

Showing results.

	Title	Accession	Instrument	Total(Mb)	Date
	{{ 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.

Raw FastQ Download URLs

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 }}

Bash script for downloading FastQ files

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 }}

Aspera commands for downloading FastQ files

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

key path

Rename?

Append mv command to rename downloaded files Don't rename files

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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 }}

Cluster Flow FastQ download file (nice filenames)

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 }}

bcbio project file for FastQ downloads (nice filenames)

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.

Raw SRA Download URLs

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

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

Bash script for downloading SRA files (nice filenames)

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 }}

Cluster Flow SRA download file (nice filename)

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.

TSV

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 }}

JSON

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

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{{ savedResultsENAfastq | json }}

YAML

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

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{{ savedResultsENAfastqYAML }}

Query URL =

Source code is available under a GNU GPLv3 licence at https://github.com/ewels/sra-explorer.