Portable nanopore analytics: are we there yet? | Zendy

Marco Antônio Oliva | Zendy; Franco Milicchio | Zendy; Kaden King | Zendy; Grace Benson | Zendy; Christina Boucher | Zendy; Mattia Prosperi | Zendy

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Portable nanopore analytics: are we there yet?

Author(s) -

Marco Antônio Oliva,

Franco Milicchio,

Kaden King,

Grace Benson,

Christina Boucher,

Mattia Prosperi

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa237

Subject(s) - analytics , nanopore , computer science , data science , software , computational biology , nanotechnology , biology , materials science , programming language

Several tools, from base-calling to genome assembly, were ported and benchmarked on an Android smartphone. Out of 23 programs, 11 succeeded. Recompilation failures included lack of standard headers and unsupported instruction sets. Only DSK, BCALM2 and Kraken were able to process files up to 16GB, with linearly scaling CPU-times. However, peak CPU temperatures were high. In conclusion, the portability scenario is not favorable. Given the fast market growth, attention of developers to ARM chipsets and Android/iOS is warranted, as well as initiatives to implement mobile-specific libraries.

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