run_bowtie2: Run the Bowtie2

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

Run the Bowtie2

Description

Runs the Bowtie2 tool

Usage

run_bowtie2(
  input1 = NULL,
  input2 = NULL,
  index = NULL,
  sample.name = NULL,
  out.dir = NULL,
  threads = 10,
  end2end = FALSE,
  sensitive = FALSE,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  bowtie2 = NULL,
  version = FALSE
)

Arguments

input1	List of the paths to files containing to the forward reads
input2	List of the paths to files containing to the reverse reads
index	Path to the reference genome index
sample.name	List of the sample names
out.dir	Name of the directory from the Bowtie2 output
threads	Number of threads for Bowtie2 to use, default set to 10
end2end	Select presets for end to end alignments
sensitive	Select the very sensitive preset
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
bowtie2	Path to the Bowtie2 program
version	Returns the version number

Value

A list with the Bowtie2 commands

Examples

## Not run: 
path <- "/software/bowtie_v2-2.3.5.1/bowtie2"

bowtie2.version <- run_bowtie2(bowtie2 = path,
                               version = TRUE)
bowtie2.version[1]

out <- "bowtie2_alignments"
trimmed_reads_dir <- "trimmed_reads"

mate1 <- list.files(path = trimmed_reads_dir,
                    pattern = "*_R1_001.fastq$",
                    full.names = TRUE)
mate2 <- list.files(path = trimmed_reads_dir,
                   pattern = "*_R2_001.fastq$",
                   full.names = TRUE)
sample.names <- unlist(lapply(strsplit(list.files(path = trimmed_reads_dir,
                                                  pattern = "*_R1_001.fastq$",
                                                  full.names = FALSE),"_"), `[[`, 1))
index <- "/export/jessie3/gmh5n/BactoCap/JoHalliday/Project1543/MLSTReference/MLST"

bowtie2.cmds <- run_bowtie2(input1 = mate1,
                            input2 = mate2,
                            index = index,
                            out.dir = out,
                            sample.name = sample.names,
                            bowtie2 = path,
                            version = FALSE)
bowtie2.cmds

## End(Not run)

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