Implementation of an "insertion-only" mode

[leon8889]

A friend of mine recommended me BreaKmer for identification of insertions. Now I recognized that BreaKmer is always search for all kinds of structural variants. Would it be possible to implement some kind of "insertion only" mode to speed everything up?

[ryanabo]

The time-consuming process is in reconstructing the contigs and remapping them. You would not necessarily know which contigs contained insertions or other types of SVs until those steps are done. So, in the end the method would not significantly change.