I noticed there have been questions related to plasmid assembly popping up periodically, so I wanted to introduce you guys to our new tool, Recycler. Recycler takes assembly graphs output by recent versions of SPAdes and uses them to search for likely plasmids in isolate samples, metagenomes, and purified plasmidome data. The tool is freely available here: https://github.com/Shamir-Lab/Recycler
For those that want full details, the manuscript is here: http://biorxiv.org/content/early/2016/04/05/029926
Our tests and feedback from early users indicate Recycler's outputs are real, and we are conducting extensive biological validation of predicted plasmids. We welcome any feedback, and hope the tool helps advance the study of plasmids!