we are trying to identify the content of a large insertion localized at a known place in the human genome. Do you know an existing software that is able to start and extend a de-novo assembly from a read mapped to the REF sequence ?
* my collaborators have sequenced the region of interest using IOn-torrent + mate-pair. As far as I can see, there are a lot of mismatches in the aligned reads.
* my BWA alignement returns a poor depth in the region of interest (~ 2 )
* CGH shows that the insertion is a junction of a head-to-head duplication