diff --git a/_gsocproposals/2025/proposal_GeneROOT.md b/_gsocproposals/2025/proposal_GeneROOT.md new file mode 100644 index 000000000..20c2151a9 --- /dev/null +++ b/_gsocproposals/2025/proposal_GeneROOT.md @@ -0,0 +1,55 @@ +--- +title: Using ROOT in the field of genome sequencing +layout: gsoc_proposal +project: ROOT +year: 2025 +difficulty: medium +duration: 350 +mentor_avail: June-November +organization: + - CERN + - CompRes +--- + +## Description + +The [ROOT](https://root.cern/) is a framework for data processing, born at CERN, +at the heart of the research on high-energy physics. Every day, thousands of +physicists use ROOT applications to analyze their data or to perform +simulations. The ROOT software framework is foundational for the HEP ecosystem, +providing capabilities such as IO, a C++ interpreter, GUI, and math +libraries. It uses object-oriented concepts and build-time modules to layer +between components. We believe additional layering formalisms will benefit ROOT +and its users. + +ROOT has broader scientific uses than the field of high energy physics. Several +studies have shown promising applications of the ROOT I/O system in the field +of genome sequencing. This project is about extending the developed capability +in [GeneROOT](https://github.com/GeneROOT) and understanding better the +requirements of the field. + + +## Expected results +* Reproduce the results based on previous comparisons against ROOT master +* Investigate and compare the latest compression strategies used by [Samtools](https://www.htslib.org/) for conversions to BAM, with RAM(ROOT Alignment Maps). +* Explore ROOT's [RNTuple](https://root.cern/doc/v622/md_tree_ntuple_v7_doc_README.html) format to efficiently store RAM maps, in place of the previously used `TTree`. +* Investigate different ROOT file splitting techniques +* Produce a comparison report + + +## Requirements +* C++ and Python programming +* Familiarity with Git +* Knowledge of ROOT and/or the BAM file formats is a plus. + + +## Mentors +* [Martin Vasilev](mailto:mvassilev@uni-plovdiv.bg) +* [Jonas Rembser](mailto:Jonas.Rembser@cern.ch) +* [Fons Rademakers](mailto:Fons.Rademakers@cern.ch) + + +## Links +* [Latest Presentation on GeneROOT](https://indico.cern.ch/event/655464/) +* [ROOT](https://root.cern/) +* [GeneROOT](https://github.com/GeneROOT)