a50

Compare genome assemblies

http://blog.malde.org/index.php/a50-a-graphical-comparison-of-genome-assemblies

Latest on Hackage:0.5

This package is not currently in any snapshots. If you're interested in using it, we recommend adding it to Stackage Nightly. Doing so will make builds more reliable, and allow stackage.org to host generated Haddocks.

LicenseRef-GPL licensed by Ketil Malde
Maintained by Ketil Malde

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.