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.