baseLess: lightweight detection of sequences in raw MinION data

Bioinformatics Advances, vol. 3, pp. vbad017

Abstract

Summary: With its candybar form factor and low initial investment cost, the MinION brought affordable portable nucleic acid analysis within reach. However, translating the electrical signal it outputs into a sequence of bases still requires mid-tier computer hardware, which remains a caveat when aiming for deployment of many devices at once or usage in remote areas. For applications focusing on detection of a target sequence, such as infectious disease monitoring or species identification, the computational cost of analysis may be reduced by directly detecting the target sequence in the electrical signal instead. Here, we present baseLess, a computational tool that enables such target-detection-only analysis. BaseLess makes use of an array of small neural networks, each of which efficiently detects a fixed-size subsequence of the target sequence directly from the electrical signal. We show that baseLess can accurately determine the identity of reads between three closely related fish species and can classify sequences in mixtures of 20 bacterial species, on an inexpensive single-board computer. Availability and implementation: baseLess and all code used in data preparation and validation are available on Github at https://github.com/cvdelannoy/baseLess, under an MIT license. Used validation data and scripts can be found at https://doi.org/10.4121/20261392, under an MIT license. Supplementary information: online.

Authors 6

1. Ben Noordijk

   Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University , Wageningen 6700AH, The Netherlands

2. Reindert Nijland

   Wageningen University & Research

   Affiliation as printed

   Marine Animal Ecology, Wageningen University , Wageningen 6700AP, The Netherlands

3. Víctor J. Carrión Aachen Institute of Biology, Leiden University

   Leiden University · Consejo Superior de Investigaciones Científicas · Universidad de Málaga · Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" · Netherlands Institute of Ecology

   Affiliation as printed

   Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC) , Málaga 29010, Spain

   Department of Microbial Ecology, Netherlands Institute of Ecology , Wageningen 6700AB, The Netherlands

   Institute of Biology, Leiden University , Leiden 2300RA, The Netherlands

4. Jos M. Raaijmakers Aachen Institute of Biology, Leiden University

   Leiden University · Netherlands Institute of Ecology

   Affiliation as printed

   Department of Microbial Ecology, Netherlands Institute of Ecology , Wageningen 6700AB, The Netherlands

   Institute of Biology, Leiden University , Leiden 2300RA, The Netherlands

5. Dick de Ridder

   Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University , Wageningen 6700AH, The Netherlands

6. Carlos Victor de Lannoy corresponding

   Delft University of Technology · Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University , Wageningen 6700AH, The Netherlands

   Department of Bionanoscience, Delft University of Technology , Delft 2600GA, The Netherlands