Many of you are familiar with EMIRGE, a software for reconstruction 16S rRNA genes from shotgun data. I've been trying to use EMIRGE for my own research, however the software is buggy and not that well supported. I've seen Megraft but authors claim it's not going to work well with data from Illumina.
Are there any other packages worth trying? I like a lot the idea of targeted reconstruction (saves time and increases sensitivity), but there no software packages to choose from to solve that task.