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PHONI: Streamed Matching Statistics with Multi-Genome References

Citation Author(s):
Christina Boucher, Travis Gagie, Tomohiro I, Dominik Koeppl, Ben Langmead, Giovanni Manzini, Gonzalo Navarro, Alejandro Pacheco, Massimiliano Rossi
Submitted by:
Dominik Koeppl
Last updated:
24 February 2021 - 9:27pm
Document Type:
Presentation Slides
Document Year:
2021
Event:
Categories:

Abstract 

Abstract: 

Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this case, which Rossi et al. recently implemented, but it uses two passes over the patterns and buffers a pointer for each character during the first pass. In this paper, we simplify their solution and make it streaming, at the cost of slowing it down slightly. This means that, first, we can compute the matching statistics of several long patterns (such as whole human chromosomes) in parallel while still using a reasonable amount of RAM; second, we can compute matching statistics online with low latency and thus quickly recognize when a pattern becomes incompressible relative to the database. Our code is available at https://github.com/koeppl/phoni .

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