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
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.
DISCOVAR takes 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 The blog and manual contained references to fragments of size 700 bp, which were outdated, and have now been removed.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.
We’ve added a key purification step “A second 0.7x SPRI clean up was performed following adapter ligation to remove adapter dimers and library fragments below ~150 bp in size.” This improves performance.
Revision 46631 contains a number of algorithmic improvements. In particular there are now less ‘false’ bubbles in assemblies. These arise particularly in assemblies at high (> 60x) coverage, as one might have e.g. for a bacterium. These bubbles have substantial support on both branches but examination of the quality score distributions of the read bases associated with both allows DISCOVAR to kill off one branch.