run_masurca: Run the MaSuRCA assembly program

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

Run the MaSuRCA assembly program

Description

@description Creates a shell script to perform the hybrid assembly an correction of illumina and either nanopore or pacbio reads

Usage

run_masurca(
  input1 = NULL,
  input2 = NULL,
  input_long = NULL,
  output = NULL,
  threads = 10,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  masurca = NULL,
  version = FALSE
)

Arguments

input1	List of the paths to files containing to the forward reads, can be gzipped
input2	List of the paths to files containing to the reverse reads, can be gzipped
input_long	List of the paths to files containing the nanopore ot pacbio read, can be gzipped
output	Name of assembly script, default assemble.sh
threads	Number of threads
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
masurca	Path to the masurca program, required
version	Returns the version number

Value

A list with the masurca commands

Examples

## Not run: 
# Path to masurca executable file
 path <- "/software/MaSuRCA-4.1.1/bin/masurca"

 # Check the program version
 run_masurca(masurca = path,
             version = TRUE)

 # Set paths to the reads files
 fastq1 <- "illumina1.fq.gz"
 fastq2 <- "illumina2.fq.gz"
 nanopore <- "nanopore.fq.gz"

 # Run the masurca commands to create the assembly script
 run_masurca(input1 = fastq1,
             input2 = fastq2,
             input_long = nanopore,
             threads = 40,
             masurca = path)

## End(Not run)

GrahamHamilton/pipelineTools documentation built on Aug. 4, 2024, 3:18 a.m.