This tool aims to make datasets within the Sequence Read Archive more accessible.
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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' }} |
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. 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 }}
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 }}
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.
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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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| {{ x.accession }} | {{ x.title }} | {{ x.platform }} | {{ x.total_bases }} | {{ x.createdate }} | {{ x.sra_url }} | {{ x.accession }}.sra | {{ x.sra_niceFilename }} | {{ x.fastq_url }} | {{ x.fastq_asperaurl }} | {{ x.fastq_filename }} | {{ x.fastq_niceFilename }} |
Query URL =