rPhrap Graph Script Documentation 0

rPhrap version 4.23 and higher

Post-processing Graphics Files
Contigimage
Graphimage
Histimage

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Post-processing Graphics Files
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With rPhrap are included a set of stand-alone Perl scripts that can be used to analyze and visualize some of the output rPhrap generates. Both Perl and the GD Perl module must be installed on your system in order for these graphing programs to be operational.

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Contigimage
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Contigimage is a Perl script that processes the .ace file (obtained by running rPhrap with the "-new_ace" option) to produce contig alignment graphs. The script takes the .ace file as the only command-line argument and produces contig layouts in a new sub-directory named for the root of the .ace filename. If the .ace file is foo.ace, then the command:

contigimage foo.ace

will create a sub-directory in the current directory called foo.images, if it does not already exist. The contig images will be placed in this directory. The contigs are displayed at 1000 positions per image. Contigs longer than 1000 are split into multiple images. The image files are named contig_name.image_number.png. The image_number is not present for contigs less than 1000 bases total length.

The qualities at each position and the consensus are expressed by the relative heights of the colored bars representing the reads and consensus. Reads extending beyond the range of each image are shown with directional arrows indicating extension.

Complemented reads are shown in color. The .png images can be viewed with "xview", a free viewer available for download, with "Preview" on Mac OS X, or directly with the latest web browsers.

Contigimage uses the freeware graphics packages GD and Perl. Both of these packages must be installed on your system. Both are available as free downloads on the Internet (http://search.cpan.org, http://www.boutell.com/gd).

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