copy_assemble

Assembles a small number of overlapping DNA sequences into their respective gene copies.

Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.

Lei Yang

copyseparator

Assembling Long Gene Copies from Short Read Data

copy_assemble function

<dl><dt>filename</dt>
<dd>A fasta alignment of a small number of overlapping DNA sequences (results from "copy_separate") covering the entire length of the target gene. Check the alignment carefully before proceeding.</dd>
<dt>copy_number</dt>
<dd>An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies. Must be the same value as used for "copy_separate".</dd>
<dt>verbose</dt>
<dd>Turn on (verbose=1; default) or turn off (verbose=0) the output.</dd></dl>

Arguments

copy_assemble — copy_assemble

<dl>

<dt>filename</dt>
<dd>A fasta alignment of a small number of overlapping DNA sequences (results from "copy_separate") covering the entire length of the target gene. Check the alignment carefully before proceeding.</dd>


<dt>copy_number</dt>
<dd>An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies. Must be the same value as used for "copy_separate".</dd>


<dt>verbose</dt>
<dd>Turn on (verbose=1; default) or turn off (verbose=0) the output.</dd>

</dl>

copy_assemble: copy_assemble

Description

Usage

Value

Arguments

Examples