A function to execute seqtk trimming

This function executes a ubuntu docker that remove reads shorter of a specific threshold

trimFasta(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  min.length = 300
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs

scratch.folder,

a character string indicating the path of the scratch folder

data.folder,

a character string indicating the folder where input data are located and where output will be written

min.length,

min nucleotide lenght of each fasta seq

Value

Returns a fasta file colled trimmed.fasta.gz

Author

Raffaele A Calogero, raffaele.calogero [at] unito [dot] it, University of Torino. Italy

Examples

if (FALSE) {
    #running fastq2fasta
    trimfasta(group="docker", scratch.folder="/data/scratch", data.folder=getwd(), min.length=300)
}