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Efficiently merging two r-indexes

Abstract

Large sequencing projects, such as GenomeTrakr and MetaSub, are updated frequently(sometimes daily, in the case of GenomeTrakr) with new data. Therefore, it is imperativethat any data structure indexing such data supports efficient updates. Toward this goal, Bannai et al. (TCS, 2020) proposed a data structure named dynamic r-index which is suitable for large genome collections and supports incremental construction; however, it is still not powerful enough to support substantial updates. Here, we develop a novel algorithm for updating ther-index, which we refer to as rimerge. Fundamental to our algorithm is the combination of the basics of the dynamic r-index with a known algorithm for merging Burrows-Wheeler Transforms (BWTs). As a result, rimerge is capable of performing batch updates in a manner that exploits parallelism while keeping the memory overhead small. We compare our method to the dynamic r-index of Bannai et al. using two different datasets, and show that rimerge is between 1.88 to 5.34 times faster on reasonably large inputs.

Download and run

In order to compile and run rimerge run the following:

git clone https://github.com/marco-oliva/rimerge
cd rimerge
mkdir build && cd build
cmake ..
make 
make install

This will create a bin directory where you will find rimerge

Citing

This work was supported by NIH R01AI141810 and made publicly available under GNU license. If you use any parts of the repository, please acknowledge via citation of the following publication and this repository.

@inproceedings{oliva2021efficiently,
  title={Efficiently Merging r-indexes},
  author={Oliva, Marco and Rossi, Massimiliano and Sir{\'e}n, Jouni and Manzini, Giovanni and Kahveci, Tamer and Gagie, Travis and Boucher, Christina},
  booktitle={2021 Data Compression Conference (DCC)},
  pages={203--212},
  year={2021},
  organization={IEEE}
}