copyseparator (version 1.2.0)

sep_assem: sep_assem

Description

Separates two or more gene copies from short-read Next-Generation Sequencing data into a small number of overlapping DNA sequences and assemble them into their respective gene copies.

Usage

sep_assem(
  copy_number,
  read_length,
  overlap = 225,
  rare_read = 10,
  core_number = 1,
  verbose = 1
)

Value

A fasta alignment of the anticipated number of full-length gene copies.

Arguments

copy_number

An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies in the input file.

read_length

An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length >=250bp.

overlap

An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets. Default 225.

rare_read

A positive integer. During clustering analyses, clusters with less than this number of reads will be ignored. Default 10.

core_number

An integer describing number of cores to use.

verbose

Turn on (verbose=1; default) or turn off (verbose=0) the output.

Examples

if (FALSE) {
sep_assem(2,300,225,10,1,1) # all input fasta files in the working directory will be processed
}