Initial computational methods for analyzing restriction site associated DNA markers (RAD-seq) were designed for either single end sequencing or for contigs assembled from single digest RADs. However, new methods using double digests (e.g., ddRAD-seq) produce RADs where individual PE reads are non-overlapping.
To address this problem this software independently infers contigs for each R1 and R2 read using rainbow. Contigs representing read pairs are then associated based on read mapping positions. After contigs are paired all contigs are merged into a pseudo-genome (= RADnome). Individual samples are then mapped to this RADnome and software packages such as GATK can be used to identify SNVs.
Update 7/7/13: We're releasing a beta version (0.0.1). You can read the instructions here. We'll be updating this code set rapidly over the next few days, but feel free to play around with it.
Update 7/1/13: We're still hammering out a few bugs and making sure everything is spick-and-span for the first release. Everything thing should be ready to go by Friday July 5th. Sorry for the delay and stay tuned.
Original Post, circa 6/25/13: RADnome is still in development. However, we expect to have a working pipeline in place by July 1st 2013. Follow us on twitter or github and we'll let you know when everything is ready to go.
- Email: RADnome@gmail.com
- Twitter: RADnome
- Github: github.com/ngcrawford/RADnome
This project was conceived W. Brian Simison (@wbsimey) and Nicholas Crawford (@ngcrawford) with contributions from Josh Pollock (@iliketurkey).