The a50 package
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.
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|Versions||0.2, 0.4, 0.5|
|Dependencies||base (>=3 && <5), biofasta, biopsl, cmdargs (>=0.5), containers, directory, process [details]|
|Maintainer||Ketil Malde <firstname.lastname@example.org>|
|Uploaded||Tue Jul 23 20:36:12 UTC 2013 by KetilMalde|
|Downloads||832 total (6 in the last 30 days)|
|Status||Docs not available [build log]
Last success reported on 2015-12-08 [all 7 reports]
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