sep_assem: sep_assem

In copyseparator: Assembling Long Gene Copies from Short Read Data

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
)

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.

Value

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

Examples

## Not run: 
sep_assem(2,300,225,10,1,1) # all input fasta files in the working directory will be processed

## End(Not run)

copyseparator documentation built on Nov. 25, 2022, 1:06 a.m.