Software
Most of my software can be found at my github page. Below you can find a list of my main projects.
ebwt2InDel
ebwt2InDel is a tool implementing a novel algorithm for finding SNPs/INDELs in a set of reads by processing just the BurrowsWheeler transform (BWT) of the input. The tool is based on the observations that, in the BWT, SNPs and INDELs are clustered since they share the same context. The tool also implements a novel succinct suffixarray navigation algorithm. Publications:

Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone, 2019. SNPs detection by eBWT positional clustering. Algorithms for Molecular Biology, 14(1), p.3.

Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone, 2018. Detecting mutations by eBWT. In 18th International Workshop on Algorithms in Bioinformatics, (WABI 2018). Vol. 113, pp. 115. Schloss DagstuhlLeibnizZentrum fur Informatik GmbH, Dagstuhl Publishing.

Nicola Prezza and Giovanna Rosone, 2019. SpaceEfficient Computation of the LCP Array from the BurrowsWheeler Transform. arXiv preprint arXiv:1901.05226
rindex
The rindex is the first fulltext index of size O(r), r being the number of BWT runs of the input text (of size n), supporting nearoptimal locate of pattern occurrences. The rindex employs a novel suffix array sampling of size 2r; in classical FMindexes, this sampling would result in a locate time of Omega(n/r) per occurrence. The rindex, on the other hand, reduces this time to O(log(n/r)).
DYNAMIC
DYNAMIC is a C++ library offering space and timeefficient implementations of some basic succinct/compressed dynamic data structures such as succinct dynamic partial sums, bitvectors, strings.
ERNE 2
This tool, developed in collaboration with the university of Udine and the Institute of Applied Genomics, includes:
 A DNA shortreads aligner.
 A bisulfitetreated shortreads aligner for methylation analysis.
 A read filtering tool.
 A methylation calling tool.
ERNE is based on a novel succinct hash data structure combining the concepts of BurrowsWheeler transform and HammingAware hash functions.