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