The a50 package

[Tags: gpl, program]

a50 - a simple tool for graphing genome coverage and fragmentation.

Reads files of contigs, and compares them by plotting each as a line in a graph. The x-axis represents contig number, the y-axis represents total (cumulative) size. An ideal assembly contains a few, large contigs, thus this curve should rise steeply, and stop early (but at the expected genome size). Conversely, a poor assembly consisting of many small fragments will have a less steep curve extending far to the right.

The graphs produced by a50 gives a simple and easy to grasp comparison between assemblies, and yet produces a more detailed and informative view than the usual metrics like largest contig size or N50.

The Darcs repository is at http://malde.org/~ketil/biohaskell/a50.


Properties

Versions0.2, 0.4, 0.5
Dependenciesbase (>=3 && <5), bio (>0.4), cmdargs (>=0.5), containers, directory, process
LicenseGPL
AuthorKetil Malde
MaintainerKetil Malde <ketil@malde.org>
CategoryBioinformatics
Executablesa50
Upload dateWed Oct 20 10:15:57 UTC 2010
Uploaded byKetilMalde
Downloads297 total (22 in last 30 days)

Downloads

Maintainers' corner

For package maintainers and hackage trustees