Portable nanopore analytics: are we there yet?

ABSTRACT:

Motivation

Oxford Nanopore technologies (ONT) add miniaturization and real time to high-throughput sequencing. All available software for ONT data analytics run on cloud/clusters or personal computers. Instead, a linchpin to true portability is software that works on mobile devices of internet connections. Smartphones' and tablets' chipset/memory/operating systems differ from desktop computers, but software can be recompiled. We sought to understand how portable current ONT analysis methods are.

Results

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 16 GB, 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.

Availability and implementation

The source code is freely available at: https://github.com/marco-oliva/portable-nanopore-analytics.

SUBMITTER: Oliva M 

PROVIDER: S-EPMC7828464 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature