Bug in superbubble removal

chanzuckerberg / shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Other

272 stars 59 forks source link

Bug in superbubble removal #212

Closed paoloczi closed 3 years ago

paoloczi commented 3 years ago

There is a bug in the algorithm that chooses assembly paths during superbubble removal (under control of command line option --MarkerGraph.simplifyMaxLength). The code does not always chooses the optimal path. This can occasionally result in locally low assembled accuracy. There is no quantitative estimate of the effect of this bug on assembled accuracy, but the events where the bug has an effect are believe to be relatively infrequent.

paoloczi commented 3 years ago

This bug is present in Shasta 0.6.0 and previous releases. It is fixed in the latest code and the fix will be available in the next release. To download a current test build containing the fix, follow the directions here.

paoloczi commented 3 years ago

The fix is in Shasta release 0.7.0.