Seqkit

Seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Citation

Citation: 10.1371/journal.pone.0163962

Environment

This tool uses the following conda environment:

Channels: - bioconda - conda-forge

Dependencies: - seqkit=2.6.1

Installation

This tool will be automatically installed when first used:

library(ShennongTools)

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

Available Commands

seq

Print basic statistics or manipulate FASTA/Q sequences

Basic Usage:

result <- sn_run("seqkit", "seq",
  # Add your parameters here
)

stats

FASTA/Q file statistics

Basic Usage:

result <- sn_run("seqkit", "stats",
  # Add your parameters here
)

grep

Search sequences by ID or pattern

Basic Usage:

result <- sn_run("seqkit", "grep",
  # Add your parameters here
)

fx2tab

Convert FASTA/Q to tab-delimited table

Basic Usage:

result <- sn_run("seqkit", "fx2tab",
  # Add your parameters here
)

rmdup

Remove duplicate sequences

Basic Usage:

result <- sn_run("seqkit", "rmdup",
  # Add your parameters here
)

Examples

Seq Example

library(ShennongTools)

result <- sn_run("seqkit", "seq",
  input = "input_file.txt"
)

# 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")
}

Stats Example

library(ShennongTools)

result <- sn_run("seqkit", "stats",
  input = "input_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")
}

Grep Example

library(ShennongTools)

result <- sn_run("seqkit", "grep",
  input = "input_file.txt"
)

# 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")
}

Fx2tab Example

library(ShennongTools)

result <- sn_run("seqkit", "fx2tab",
  input = "input_file.txt"
)

# 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")
}

Rmdup Example

library(ShennongTools)

result <- sn_run("seqkit", "rmdup",
  input = "input_file.txt"
)

# 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

seq Parameters

Inputs:

Parameter	Type	Required	Description
input	fasta, fastq	Yes	Input FASTA/Q file

Outputs:

Parameter	Type	Required	Description
output	fasta, fastq	No	Output file (stdout by default)

Parameters:

Parameter	Type	Default	Description
id	string	“”	Only print sequences with this ID
head	integer	0	Print first N records (0 = all)
tail	integer	0	Print last N records (0 = all)
extras	string	“”	Additional parameters

stats Parameters

Inputs:

Parameter	Type	Required	Description
input	fasta, fastq	Yes	Input FASTA/Q file

Outputs:

Parameter	Type	Required	Description
output	tsv	No	Output summary table (stdout by default)

Parameters:

Parameter	Type	Default	Description
threads	integer	4	Number of threads
extras	string	“”	Additional arguments

grep Parameters

Inputs:

Parameter	Type	Required	Description
input	fasta, fastq	Yes	Input FASTA/Q file

Outputs:

Parameter	Type	Required	Description
output	fasta, fastq	No	Output FASTA/Q file

Parameters:

Parameter	Type	Default	Description
pattern	string	“”	Pattern or ID to match
use_regex	boolean	FALSE	Use regular expressions
extras	string	“”	Additional grep options

fx2tab Parameters

Inputs:

Parameter	Type	Required	Description
input	fasta, fastq	Yes	Input file

Outputs:

Parameter	Type	Required	Description
output	tsv	No	Tab-separated output (stdout by default)

Parameters:

Parameter	Type	Default	Description
only_seq	boolean	FALSE	Only output sequence (no ID/desc)
extras	string	“”	Additional options

rmdup Parameters

Inputs:

Parameter	Type	Required	Description
input	fasta, fastq	Yes	Input file

Outputs:

Parameter	Type	Required	Description
output	fasta, fastq	No	Deduplicated output

Parameters:

Parameter	Type	Default	Description
by_seq	boolean	TRUE	Remove by sequence rather than ID
extras	string	“”	Additional rmdup options