By developing Akron-seq, a novel approach that captures the native 3′ and 5′ ends of capped and polyadenylated RNAs, respectively, we showed that canonical human mRNAs are subject to repeated cotranslational and ribosome-phased endonucleolytic cuts at the exit site of the mRNA ribosome channel, in a process that we termed ribothrypsis. Source code for ribothrypsis analysis has been deposited on GitHub.
CLIPSeqTools is a collection of command line applications used for the analysis of CLIP-Seq datasets. CLIP-Seq stands for UV cross-linking and immunoprecipitation coupled with high-throughput sequencing. The source code has been deposited on GitHub and a webpage with documentation and usage examples has been created.
GenOO is an open-source; object-oriented Perl framework specifically developed for the design of High Throughput Sequencing (HTS) analysis tools. The source code has been deposited on GitHub.