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 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.
Thanks to new data compression methods, our latest DISCOVAR de novorelease (50963) reduces the peak memory required for large genomes. The exact peak memory required depends on a number of factors, including the nature of the genome and the quality of the data, but is mostly determined by coverage and genome size.
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.
DISCOVAR and DISCOVAR de novo take as input read pairs from fragments of size 400-500 bp, with some larger and some smaller. The blog and manual contained references to fragments of size 700 bp, which were outdated, and have now been removed. Note that the protocol yields a wide size distribution, including some large fragments.
A DISCOVAR de novo assembly is a graph. A typical assembly consists almost entirely of linear stretches, typically like this
which we call ‘lines’, and providing a rich data type that captures polymorphism and other important features. Further, with some loss of information, these lines may be ‘flattened’ into standard contigs. We have added a tutorial explaining how these data types are available as part of the DISCOVAR output. We are also interested in hearing your thoughts regarding the utility of these output types and others that might be useful to you.