copy_validate

A tool to help identify incorrectly assembled chimeric sequences.

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_validate function

<dl><dt>filename</dt>
<dd>A DNA alignment in fasta format that contains sequences of two or more gene copies (e.g. results from "copy_assemble").</dd>
<dt>copy_number</dt>
<dd>An integer (e.g. 2,3, or 4) giving the number of gene copies in the input file.</dd>
<dt>read_length</dt>
<dd>An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data.</dd>
<dt>verbose</dt>
<dd>Turn on (verbose=1; default) or turn off (verbose=0) the output.</dd></dl>

Arguments

copy_validate — copy_validate

<dl>

<dt>filename</dt>
<dd>A DNA alignment in fasta format that contains sequences of two or more gene copies (e.g. results from "copy_assemble").</dd>


<dt>copy_number</dt>
<dd>An integer (e.g. 2,3, or 4) giving the number of gene copies in the input file.</dd>


<dt>read_length</dt>
<dd>An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data.</dd>


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

</dl>

copy_validate: copy_validate

Description

Usage

Value

Arguments

Examples