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.
Properties
| Versions | 0.2, 0.4 |
|---|---|
| Dependencies | base (≥3 & <5), bio (>0.4), cmdargs (≥0.5), containers, directory, process |
| License | GPL |
| Author | Ketil Malde |
| Maintainer | Ketil Malde <ketil@malde.org> |
| Category | Bioinformatics |
| Executables | a50 |
| Upload date | Wed Oct 20 10:15:57 UTC 2010 |
| Uploaded by | KetilMalde |
Downloads
- a50-0.2.tar.gz (Cabal source package)
- package description (included in the package)