Each DISCOVAR de novo assembly will now come with a plot like thisshowing the observed size distribution for the fragments defined by the input read pairs, and in the file frags.dist.png. These plots can be highly diagnostic. They will be available as of revision 51283. The raw data are in the file frags.dist.
Our manuscript “Comprehensive variation discovery in single human genomes” is now available as an advance online publication from Nature Genetics. This paper describes our assembly and variant calling algorithm DISCOVAR, which is able to find many novel variants missing from standard call sets. DISCOVAR is available for download now, and we encourage you to try it out. For de novo assembly without variant calling, see our other package: DISCOVAR de novo.
You can now limit the maximum number of threads DISCOVAR de novo uses with the new option
NUM_THREADS (release 51183). This is useful if you have to share your hardware, or if your system admin has limited the number of threads a single process can use. It can also be a good idea to restrict the number of threads if your hardware has many cores (>50), as the parallelization efficiency can start to drop due to locking and cache coherency issues.
We have fixed the bug in DISCOVAR de novo cited in the last blog message. Please download and use the new version (50964) from our ftp site.
We found a serious bug in DISCOVAR de novo, revision 50862, resulting in data corruption in some cases. We will correct this bug as soon as possible. In the meantime we are rolling back to revision 50693. And needless to say, we are beefing up our release testing.
The latest release (50893) of DISCOVAR de novo now supports BAM files directly, and no longer requires SAMtools to be installed. This change has the added benefit of halving the time required to import data from a BAM, potentially saving hours on a human sized genome. Note that the original variant calling version of DISCOVAR still requires SAMtools in order to work.
We’ve made some minor changes to DISCOVAR de novo output files to make them easier to use. See the manual or the Edge, lines and scaffolds primer for more details.
The assembly graph can be large, complex and unwieldy, so DISCOVAR de novo does not generate a viewable graph directly. Instead we have developed an interactive tool that allows you to explore your assembly by creating smaller viewable graphs of the regions you are interested in. This new tool, called NhoodInfo, is now part of the DISCOVAR package, as of release 50612 . It is also the engine behind our online demo, so you can try it out right now without having to create an assembly of your own. Full instructions on using NhoodInfo are included in the DISCOVAR package.