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Moni website  

MONI index uses the prefix-free parsing of the text [2][3] to build the Burrows-Wheeler Transform (BWT) of the reference genomes, the suffix array (SA) samples at the beginning and at the end of each run of the BWT, and the threshold positions of [1].

Environment Modules

Run module spider Moni to find out what environment modules are available for this application.

System Variables

  • HPC_MONI_DIR - installation directory
  • HPC_MONI_BIN - executable directory


If you publish research that uses Moni you have to cite it as follows:

[1] Hideo Bannai, Travis Gagie, and Tomohiro I, "Refining ther-index", Theoretical Computer Science, 812 (2020), pp. 96–108

[2] Christina Boucher, Travis Gagie, Alan Kuhnle and Giovanni Manzini, "Prefix-Free Parsing for Building Big BWTs", In Proc. of the 18th International Workshop on Algorithms in Bioinformatics (WABI 2018).

[3] Christina Boucher, Travis Gagie, Alan Kuhnle, Ben Langmead, Giovanni Manzini, and Taher Mun. "Prefix-free parsing for building big BWTs.", Algorithms for Molecular Biology 14, no. 1 (2019): 13.