run_bwa: Run the BWA aligner

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

Run the BWA aligner

Description

Runs the BWA aligner

Usage

run_bwa(
  command = NULL,
  input1 = NULL,
  input2 = NULL,
  index = NULL,
  sample.name = NULL,
  out.dir = NULL,
  threads = 10,
  seed.length = NULL,
  parallel = FALSE,
  cores = 4,
  execute = TRUE,
  bwa = NULL,
  version = FALSE
)

Arguments

command	BWA command to run, at present can choose 'mem', which is most useful fo Illumina, PacBio and Nanopore reads, required
input1	List of the paths to files containing to the forward reads, required
input2	List of the paths to files containing to the reverse reads, required for paired end sequence data
index	Path to the indexed reference genome, required
sample.name	List of sample names, required
out.dir	Name of the directory from the BWA output
threads	Number of threads for BWA to use, default set to 10
seed.length	Minimum seed length
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
bwa	Path to the bwa program, required
version	Returns the version number

Value

A list with the BWA commands

Examples

 ## Not run: 
 path <- "/software/bwa/bwa"

# Get version number
bwa.version <- run_bwa(bwa = path,
                       version = TRUE)
bwa.version[3] # print the line with version number

reads.path <- "/path/to/fastqs"
reads.patt.1 <- "_S\\d{1,2}\\_L001_R1_001.fastq.gz"
reads.patt.2 <- "_S\\d{1,2}\\_L001_R2_001.fastq.gz"

# Organise the samples
sample.dataframe <- prepare_samples(reads.path, c(reads.patt.1,reads.patt.2),trimmed.reads.dir)

input1 <- as.character(sample.dataframe$reads.path.1)
input1.trim <- as.character(sample.dataframe$trimmed.reads.path.1)
# Paired end only
 input2 <- as.character(sample.dataframe$reads.path.2)
 input2.trim <- as.character(sample.dataframe$trimmed.reads.path.2)

sample.names <- as.character(sample.dataframe$sample.names)

genome <- "/path/to/reference/genome"

command <- "mem"
out.dir <- "bwa_alignments"

# Paired end
pe <- run_bwa(command = command,
              input1 = mate1.trim,
              input2 = mate2.trim,
              index = genome,
              threads = 20,
              out.dir = out.dir,
              sample.name = sample.names,
              seed.length = 21,
              bwa = path)

# Single end
se <- run_bwa(command = command,
              input1 = mate1.trim,
              index = genome,
              threads = 20,
              out.dir = out.dir,
              sample.name = sample.names,
              seed.length = 21,
              bwa = path)

## End(Not run)

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