Sra Tools

Toolkit for accessing and converting SRA data

Citation

Citation: 10.1093/bioinformatics/btz664

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - sra-tools

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

# Tool will be installed automatically on first use
result <- sn_run("sra-tools", "prefetch", ...)

Available Commands

prefetch

Download SRA file from NCBI SRA database

Basic Usage:

result <- sn_run("sra-tools", "prefetch",
  # Add your parameters here
)

fasterq_dump

Convert SRA files to FASTQ format

Basic Usage:

result <- sn_run("sra-tools", "fasterq_dump",
  # Add your parameters here
)

Examples

Prefetch Example

library(ShennongTools)

result <- sn_run("sra-tools", "prefetch",
  accession = "sample_name",
  output_dir = "."
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Fasterq_dump Example

library(ShennongTools)

result <- sn_run("sra-tools", "fasterq_dump",
  accession = "sample_name",
  fastq1 = "reads.fastq.gz",
  threads = 4,
  output_dir = "."
)

# Check if successful
if (sn_is_toolcall_success(result)) {
  cat("Command completed successfully!\n")
} else {
  cat("Command failed. Check logs:\n")
  cat(readLines(result@log_file), sep = "\n")
}

Parameters Reference

prefetch Parameters

Inputs:

Parameter	Type	Required	Description
`accession`	string	Yes	SRA accession (e.g., SRR123456)

Outputs:

Parameter	Type	Required	Description
`sra_file`	sra	No	Output SRA file (stored in NCBI default location or specified path)

Parameters:

Parameter	Type	Default	Description
`output_dir`	string	“.”	Output directory to store downloaded SRA files
`extras`	string	“”	Additional options for prefetch

fasterq_dump Parameters

Inputs:

Parameter	Type	Required	Description
`accession`	string	Yes	SRA accession or path to `.sra` file

Outputs:

Parameter	Type	Required	Description
`fastq1`	fastq	Yes	First read FASTQ file (R1 or SE)
`fastq2`	fastq	No	Second read FASTQ file (R2 for paired-end)

Parameters:

Parameter	Type	Default	Description
`threads`	integer	4	Number of threads to use
`output_dir`	string	“.”	Output directory for FASTQ files
`split_files`	boolean	TRUE	Whether to split paired-end reads into two files
`extras`	string	“”	Additional options for fasterq-dump