Salmon

A tool for transcript-level quantification from RNA-seq data using quasi-mapping

Citation

Citation: 10.1038/nmeth.4197

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - salmon

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

# Tool will be installed automatically on first use
result <- sn_run("salmon", "index", ...)

Available Commands

index

Build a Salmon transcriptome index

Basic Usage:

result <- sn_run("salmon", "index",
  # Add your parameters here
)

quant

Quantify transcript abundances using a Salmon index

Basic Usage:

result <- sn_run("salmon", "quant",
  # Add your parameters here
)

Examples

Index Example

library(ShennongTools)

result <- sn_run("salmon", "index",
  transcriptome = "sequences.fasta",
  index_dir = "genome_index",
  threads = 4
)

# 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")
}

Quant Example

library(ShennongTools)

result <- sn_run("salmon", "quant",
  index_dir = "genome_index",
  read1 = "sample_R1.fastq.gz",
  quant_dir = "example_file",
  threads = 4
)

# 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

index Parameters

Inputs:

Parameter	Type	Required	Description
`transcriptome`	fasta	Yes	Transcriptome FASTA file

Outputs:

Parameter	Type	Required	Description
`index_dir`	directory	Yes	Output directory to store the index

Parameters:

Parameter	Type	Default	Description
`type`	string	“quasi”	Type of index to build (quasi or fmd)
`kmer`	integer	31	K-mer size
`threads`	integer	4	Number of threads
`extras`	string	“”	Extra options

quant Parameters

Inputs:

Parameter	Type	Required	Description
`index_dir`	directory	Yes	Path to Salmon index directory
`read1`	fastq	Yes	Read 1 FASTQ file
`read2`	fastq	No	Read 2 FASTQ file (for paired-end)

Outputs:

Parameter	Type	Required	Description
`quant_dir`	directory	Yes	Output directory for quantification results

Parameters:

Parameter	Type	Default	Description
`libtype`	string	“A”	Library type (e.g., A = auto-detect)
`threads`	integer	4	Number of threads
`validate_mappings`	boolean	TRUE	Enable stricter mapping validation
`gc_bias`	boolean	FALSE	Perform GC bias correction
`extras`	string	“”	Additional arguments