run_seqtk: Run Seqtk

In GrahamHamilton/pipelineTools: Pipeline Tools for NGS Sequence Analysis Pipelines

Run Seqtk

Description

Runs the seqtk tool

Usage

run_seqtk(
  command = NULL,
  input = NULL,
  output = NULL,
  seed = NULL,
  reverse = NULL,
  num_reads = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  seqtk = NULL
)

Arguments

command	Seqtk command to run, at present can choose from 'seq' and 'sample', required
input	List of fastq files, can be gzipped
output	list of output file names, fastq format
seed	Random seed for read selection
reverse	Reverse complament the fastq sequences
num_reads	Number of reads to output for sub sampling
parallel	Run in parallel, default set to FALSE
cores	Number of cores/threads to use for parallel processing, default set to 4
execute	Whether to execute the commands or not, default set to TRUE
seqtk	Path to the seqtk program, required

Examples

## Not run: 
num_reads <- 1000
cmd <- "sample"
seed <- 23
reads <- c("reads1.fq.gz","reads2.fq.gz")
out <- c("reads1_out.fq.","reads2_out.fq")
seqtk_path <- "/usr/bin/seqtk"

run_seqtk(command = cmd,
          input = reads,
          output = out,
          seed = seed,
          num_reads = num_reads,
          parallel = TRUE,
          cores = 2,
          execute = FALSE,
          seqtk = seqtk_path)

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Dec. 8, 2024, 3:53 p.m.