- MONI: An method that align sequence reads to a pan-genomics reference by constructing the r-index and matching statistics. Is able to build and align in sub-linear time and memory. Publicly available at: https://github.com/maxrossi91/moni. To appear in the proceedings of RECOMB 2021 and Journal of Computational Biology.
- PHONI: An online alignment method that uses the r-index and LCP in lieu of matching statistics. Publicly available at https://github.com/koeppl/phoni. In proceedings of DCC 2021.
de bruijn graph software
- BufBOSS: BuffBOSS is a succinct de Bruijn graph implementation that has dynamic characteristics (i.e., insertions and deletions using buffering). Our implementation is available at https://github.com/jnalanko/bufboss. Accepted to Computational and Structural Biotechnology.
- VariMerge: A method for constructing the colored de Bruijn graph for extremely large databases via succinct merging procedure. Publicly available at: https://github.com/cosmo-team/cosmo/tree/VARI-merge under GPLv3 license. My PhD students (Martin Muggli and Bahar Alapanhi) and I are the developers. Published at Journal of Bioinformatics and presented at ISMB/ECCB in 2019.
- Vari: A software tool that succinctly constructs and stores the colored de Bruijn graph. Publicly available at: https://github.com/cosmo-team/cosmo/tree/VARI Published in the journal of Bioinformatics in 2017. My PhD student (Martin Muggli) and I are the main developers. .
- LueVari: A method that detects single nucleotide polymorphisms in metagenomics data via the colored de Bruijn graph. Code and datasets are publicly available at https://github.com/baharpan/cosmo/ tree/LueVari. My PhD students (Martin Muggli and Bahar Alapanhi) and I are the developers. Published at RECOMB SEQ 2018.
optical mapping software
- Twin: A software method for aligning in silico digested DNA contigs to a genome wide optical ma. Publicly available at: http://www.cs.colostate.edu/twin/. Published in Proceedings of WABI in 2014. My PhD student (Martin Muggli) and I are the main developers. Cited 22 times.
- Rmapper: A de Bruijn graph Rmap assembler. Publicly available at https://github.com/kingufl/Rmapper My post-doc (Mass Rossi), PhD student (Kingshuk Mukherjee) and I are the developers. In proceedings of WABI 2020 and Algorithms in Molecular Biology.
- Kohdista: A software method for finding pairwise alignments between single molecule maps (Rmaps), which is the raw data produced by optical mapping. Publicly available at: Kohdista is available at https://github.com/mmuggli/KOHDISTA/ Published in the Proceedings of WABI 2018. My PhD student (Martin Muggli) and I are the main developers.
- Comet: A software method for detecting and correcting errors in single molecule maps (Rmaps), which assists them in being assembled into genome wide optical maps. Published in GigaScience in 2018. My PhD student (Kingshuk Mukherjee) and I are the main developers.
AMR ANALYSIS software
- AMRPlusPlus: A software pipeline that detects antimicrobial resistance genes from shotgun metagenomics data using sequence alignment. Actively used by the life science community. Publicly available at: http://megares.meglab.org/amrplusplus/latest/html/ Published at Nucleic Research Acids in 2017. Cited over 200 times since 2017.
- MegaRes: A public database of antimicrobial resistance genes. Actively used by the research community in antimicrobial resistance. Publicly available at: https://megares.meglab.org. Published at Nucleic Research Acids
- MetaMARC: A machine learning algorithm developed to predict AMR genes contained in a metagenomics sample. Publicly available at: https://github.com/lakinsm/meta-marc Published at Communications Biolog.
- aPPRove: A software method for identifying how and where a Pentatricopeptide repeatprotein belonging can bind to ribonucleic acid (RNA). For each binding event it outputs the binding site, the amino-acid-nucleotide interaction, and its statistical significance. The aPPRove web server is found at www.cs.colostate.edu/∼approve Published at PLoS ONE in 2016.
Contact the boucher lab for software support:
University of Florida CISE Department E301 CSE Building PO Box 116120 Gainesville, FL 32611