trimFasta: A function to execute seqtk trimming

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

A function to execute seqtk trimming

Description

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

Usage

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(s)

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

Examples

## Not run: 
    #running fastq2fasta
    trimfasta(group="docker", scratch.folder="/data/scratch", data.folder=getwd(), min.length=300)

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.