Ribomap is a package that generates isoform-level ribosome profiles from ribosome profiling data. Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and genomic repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. Ribomap addresses this problem by assigning reads to potential origins in the transcriptome proportional to the estimated transcript abundance. This results in a more accurate estimation of the ribosome pileup compared to naive read assignments.
Ribomap is written in c++, and is open source.
If you use Ribomap, please cite:
Hao Wang, Joel McManus and Carl Kingsford. Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abudance with Ribomap. Under review (2014).
Binaries for Mac OS X and Linux are available in the above-linked .tar.gz file. If neither of them work on your system, you can build the software from the sources from the GitHub repository.
For further details on the pre-requisites, compiling and running instructions about Ribomap, please refer to the README.
This work is funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554 to Carl Kingsford. It has been partially funded by the US National Science Foundation [CCF-1256087, CCF-1319998]; and US National Institutes of Health [R21HG006913, R01HG007104]. C.K. received support as an Alfred P. Sloan Research Fellow.