A function to execute CD-HIT — cdhit • docker4seq

This function executes a ubuntu docker that cluster minION sequences using CD-HIT

cdhit(
  group = c("sudo", "docker"),
  scratch.folder,
  data.folder,
  identity.threshold = 0.9,
  memory.limit = 30000,
  threads = 0,
  word.length = 7
)

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
identity.threshold,: sequence identity threshold, default 0.9, this is the default cd-hit's global sequence identity calculated as: number of identical bases in alignment divided by the full length of the shorter sequence
memory.limit,: memory limit in MB for the program, default 30000. 0 for unlimitted
threads,: number of threads, default 0; with 0, all CPUs will be used
word.length,: 7 for thresholds between 0.88 and 0.9 for other option see user manual cdhit

Value

Returns two files: a fasta file of representative sequences and a text file of list of clusters

Author

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

Examples

if (FALSE) {
    #running fastq2fasta
    cdhit(group="docker", scratch.folder="/data/scratch", data.folder=getwd(), identity.threshold=0.90, memory.limit=8000, threads=0, word.length=7)
}