This function executes the docker container bwa1 where BWA is installed BWA is a read alignment package that efficiently align short sequencing reads against a large reference sequence This aligner provides optimal results with DNA-seq data

xenome(
group = c("sudo", "docker"),
fastq.folder = getwd(),
scratch.folder = "/data/scratch",
xenome.folder,
seq.type = "pe",
)

## Arguments

group, a character string. Two options: "sudo" or "docker", depending to which group the user belongs a character string indicating where gzip fastq files are located a character string indicating the scratch folder where docker container will be mounted a character string indicating the folder where the indexed reference genomes generated by xenome are locates a character string indicating the type of reads to be trimmed. Two options: "se" or "pe" respectively for single end and pair end sequencing a number indicating the number of cores to be used from the application

## Value

ambiguous, both, neither, hs and mm fastq.gz files. xeno_hs_R1.fastq.gz and xeno_hs_R2.fastq.gz are fastq file free of mouse reads and are used for further analysis.

## Examples

if (FALSE) {
}