SRA_Fetch

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
Data Import	Any taxa	PHB v2.2.0	Yes	Sample-level

SRA_Fetch_PHB

The SRA_Fetch workflow downloads sequence data from NCBI's Sequence Read Archive (SRA). It requires an SRA run accession then populates the associated read files to a Terra data table.

Read files associated with the SRA run accession provided as input are copied to a Terra-accessible Google bucket. Hyperlinks to those files are shown in the "read1" and "read2" columns of the Terra data table.

Inputs

The only required input for the SRA_Fetch workflow is an SRA run accession beginning "SRR", an ENA run accession beginning "ERR", or a DRA run accession which beginning "DRR".

Please see the NCBI Metadata and Submission Overview for assistance with identifying accessions. Briefly, NCBI-accessioned objects have the following naming scheme:

STUDY	SRP#
SAMPLE	SRS#
EXPERIMENT	SRX#
RUN	SRR#

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
fetch_sra_to_fastq	sra_accession	String	SRA, ENA, or DRA accession number		Required
fetch_sra_to_fastq	cpu	Int	Number of CPUs to allocate to the task	2	Optional
fetch_sra_to_fastq	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
fetch_sra_to_fastq	docker_image	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/biocontainers/fastq-dl:2.0.4--pyhdfd78af_0	Optional
fetch_sra_to_fastq	fastq_dl_options	String	Additional parameters to pass to fastq_dl from here	"--provider sra"	Optional
fetch_sra_to_fastq	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	8	Optional
version_capture	docker	String	The Docker container to use for the task	us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0	Optional
version_capture	timezone	String	Set the time zone to get an accurate date of analysis (uses UTC by default)		Optional

Outputs

Read data are available either with full base quality scores (SRA Normalized Format) or with simplified quality scores (SRA Lite). The SRA Normalized Format includes full, per-base quality scores, whereas base quality scores have been simplified in SRA Lite files. This means that all quality scores have been artificially set to Q-30 or Q3. More information about these files can be found here.

Given the lack of usefulness of SRA Lite formatted FASTQ files, we try to avoid these by preferentially searching SRA directly (SRA-Lite is more probably to be the file synced to other repositories), but sometimes downloading these files is unavoidable. To make the user aware of this, a warning column is present that is populated when an SRA-Lite file is detected.

Variable	Type	Description
sra_fetch_version	String	The version of the repository the SRA_Fetch workflow is in
sra_fetch_analysis_date	String	The date the workflow was run
read1	File	File containing the forward reads
read2	File	File containing the reverse reads (not available for single-end or ONT data)
fastq_dl_date	String	The date of the read data download
fastq_dl_docker	String	The docker used
fastq_dl_metadata	File	File containing metadata of the provided accession such as submission_accession, library_selection, instrument_platform, among others
fastq_dl_version	String	The version of fastq-dl used
fastq_dl_warning	String	This warning field is populated if SRA-Lite files are detected. These files contain all quality encoding as Phred-30 or Phred-3.

References

fastq-dl: Petit III, R. A., Hall, M. B., Tonkin-Hill, G., Zhu, J., & Read, T. D. fastq-dl: efficiently download FASTQ files from SRA or ENA repositories (Version 2.0.2) [Computer software]. https://github.com/rpetit3/fastq-dl