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.
|Dependencies||base (≥3 & <5), bio (>0.4), cmdargs (≥0.5), containers, directory, process|
|Maintainer||Ketil Malde <firstname.lastname@example.org>|
|Upload date||Wed Oct 20 10:15:57 UTC 2010|