Goby 2 Roadmap

[Fabien Campagne]

We have used Goby file formats extensively internally at Weill Cornell to implement all sorts of analyses (i.e., RNA-Seq, exome or whole genome sequencing, RRBS for DNA methylation). Goby tools implement pipelines for differential expression, genotype calling and for detecting DNA methylation differences. These tools are integrated with GobyWeb and are heavily used at our CTSC institutions. However, until recently we had not spent a lot of time thinking about importing/exporting BAM.

This probably explains why we have not seen a lot of use of Goby outside of Cornell at this point. Indeed, the path to generate large Goby files was a bit tricky for people who did not have access to GobyWeb (which automates alignments and handles all data in Goby formats by default).  To address these problems, Goby 2 will provide:

- Direct import of SAM/BAM files to Goby. 

- Exports of Goby to BAM

- Parallel sort working on large goby alignment files (the current sort mode in Goby 1 is limited by available memory). We did not need this feature because GobyWeb already produced large sorted alignments, but we realize others who just use the command line need such a tool.

- Improved compression. 

Please let us know if you encountered other problems when taking Goby for a test run so we can address the issues and make interoperability with your current pipelines easier.