Fragment library size distribution plots

Each DISCOVAR de novo assembly will now come with a plot like this

frags.dist

showing 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 are available from revision 51298 onwards. The raw data are in the file frags.dist

DISCOVAR paper published

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.

Thread control for 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.

Native support added for BAMs in DISCOVAR de novo

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.

Peak memory improvements

Thanks to new data compression methods, our latest release (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.

Assembly graph visualization tool released

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 demoso 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.