run_flye: Run the Flye assembler

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

Run the Flye assembler

Description

Run the long read assembler Flye

Usage

run_flye(
  input = NULL,
  sample_names = NULL,
  platform = NULL,
  out_dir = NULL,
  threads = 10,
  parallel = FALSE,
  cores = 4,
  execute = FALSE,
  flye = NULL,
  version = FALSE
)

Arguments

input	List of the paths to files containing to the long reads, required
sample_names	List of sample names, required
platform	Names of the sequencing platform, choose either, pacbio_raw, PacBio regular CLR reads less than 20 percent error pacbio_corr, PacBio reads that were corrected with other methods less than 3 percent error pacbio_hifi, PacBio HiFi reads nano_raw, ONT regular reads, pre-Guppy5 less than 20 percent error nano_corr, ONT reads that were corrected with other methods less than 3 percent error nano_hq , ONT high-quality reads: Guppy5+ or Q20 less than 5 percent error
out_dir	Name of the directory from the assembled reads
threads	Number of threads for flye to use, default set to 10
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
flye	Path to the flye program, required
version	Returns the version number

Value

A list with the Flye commands

Examples

## Not run: 
path <- "/path/to/flye"
input_files <- c("sample1.fastq", "sample2.fastq")
sample_names <- gsub(".fastq","",input_files)
platform <- "nano_hq"
out_directory <- "Assemblies"

run_flye(flye = path,
         version = TRUE)

run_flye(input = input_files,
         sample_names = sample_names,
         platform = platform,
         out_dir = out_directory,
         threads = 10,
         parallel = FALSE,
         cores = 4,
         execute = FALSE,
         flye = path)

## End(Not run)

GrahamHamilton/pipelineTools documentation built on March 5, 2024, 12:23 p.m.