Oxford Nanopore RNA and DNA sequencing

Links for useful software to process ONP reads

Oxford nanopore (ONP) produces pocket size sequencers which allow for analysis of DNA and RNA in its native form hence detect not only the DNA code but also modifications of DNA and RNA, known as epigenetic modifications. Think of it as adding a dot or coma over the alphabet, these modifications are as important as the DNA and RNA code. My lab started to utilize this technique of long reads single molecule sequencing in March of 2018 and we have already achieved progress in both DNA and RNA analysis. The projects we focus right now is to identify RNA modifications which affect male infertility and use long reads DNA sequencing in diagnosis of male infertility. This is really cool technology but as with each new technology in genetics the tools to process the reads from the sequencer are being developed and are not easy to implement. I will post here the links to tools I use in processing of the long reads both DNA and RNA. Please remember that the tools are updated and rewritten almost daily so always use most up to date version of the software.

DNA processing: de-novo aligners:

https://github.com/ruanjue/smartdenovo