How does COBRA handle joining two query sequences?

[LSHillary]

Hi Linxing,

Great tool. I'm really interested in using it with some of my datasets. One question that came up in discussing COBRA with others was how it handles cases where e.g. Query Contigs Q1 and Q2 could be joined by non-query contigs, e.g. Q1-c1-c2-Q2. Apologies if I missed this part of the manuscript but does COBRA have the ability to handle this, or does it start from the assumption that it is only looking for ways it can extend query contigs in isolation?

Best,

Luke

[linxingchen]

Hi Luke,

Thank you for your interest in COBRA.

COBRA could join two or more query contigs/scaffolds if they meet some specific conditions, for example, coverage, paired reads spanning, etc.

Let me know if you have other questions, I am happy to discuss more.

Best,
LINXING