Kallisto

Quantification of transcript abundances from RNA-Seq data

Citation

Citation: 10.1038/nbt.3519

Environment

This tool uses the following conda environment:

Channels: - conda-forge - bioconda

Dependencies: - kallisto

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

index

Build a kallisto index from a transcriptome FASTA file

Basic Usage:

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

quant

Quantify transcript abundance from RNA-Seq reads using a kallisto index

Basic Usage:

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

Examples

Index Example

library(ShennongTools)

result <- sn_run("kallisto", "index",
  transcriptome = "sequences.fasta",
  index = "genome_index"
)

# 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("kallisto", "quant",
  index = "genome_index",
  read1 = "sample_R1.fastq.gz",
  output_dir = "output_file.txt",
  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 reference in FASTA format

Outputs:

Parameter	Type	Required	Description
`index`	index	Yes	Output index file for kallisto quant

Parameters:

Parameter	Type	Default	Description
`k`	integer	31	k-mer size (default is 31)
`extras`	string	“”	Additional parameters for kallisto index

quant Parameters

Inputs:

Parameter	Type	Required	Description
`index`	index	Yes	Path to kallisto index
`read1`	fastq	Yes	FASTQ file with first reads
`read2`	fastq	No	FASTQ file with second reads (for paired-end)

Outputs:

Parameter	Type	Required	Description
`output_dir`	directory	Yes	Output directory containing abundance.tsv and other results

Parameters:

Parameter	Type	Default	Description
`threads`	integer	4	Number of threads
`bootstrap_samples`	integer	0	Number of bootstrap samples to compute
`single`	boolean	FALSE	Whether reads are single-end
`fragment_length`	integer	200	Fragment length for single-end reads
`sd`	numeric	20	Standard deviation of fragment length for single-end reads
`extras`	string	“”	Additional parameters for kallisto quant