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Matthew Links

Interactive exploration of base calls in nanopore data

About Matthew Links

Matthew Links is an Assistant Professor in the Department of Animal and Poultry Science and an associate member of the Computer Science Department at the University of Saskatchewan. His interests in the microbiome have involved numerous contexts: enhanced oil recovery, the rhizosphere, infectious diseases as well as plant and animal health. In these settings Dr. Links’ work has demonstrated that cpn60 is a robust DNA barcode that can be used in microbial profiling studies and provides significant advantages over other genes commonly used for microbial profiling. Recent work has resulted in a novel enrichment technique for microbial profiling (Capture-Seq) that eliminates the need for universal PCR and dramatically reduces the amount of shotgun sequencing data required to gain quantitative information about microbiota from any ecological niche. Matthew’s current work with nanopore sequencing is focused on allowing researchers to interrogate the signal data directly. A key goal of his work is to enable visualization of signal event data in a way that allows a researcher to assess whether a base call was in error, whether the sample was actually from a mixed sample, or represents a heterozygote.

Recent publications

Albert, A. Y. K. et al. A study of the vaginal microbiome in healthy Canadian women utilizing cpn60-based molecular profiling reveals distinct Gardnerella subgroup community state types. PLoS ONE 10, (2015).

Links, M. G. et al. Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds. New Phytologist 202, 542–553 (2014).

Links, M. G., Chaban, B., Hemmingsen, S. M., Muirhead, K. & Hill, J. E. mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences. Microbiome 1, 23 (2013).

Links, M. G., Dumonceaux, T. J., Hemmingsen, S. M. & Hill, J. E. The Chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS ONE 7, (2012).

Abstract

Oxford Nanopore Technologies MinION DNA sequencer provides users with large amounts of genomic data in real-time. In addition to the sequence itself, detailed event information is available that includes signal trace, time, and model state of each nanopore. While there are sequencing errors associated with nanopore sequencing, there are not interactive ways for users to assess specific base-pair positions in terms of whether sequence variation corresponds to technical error or true biological diversity. We have developed a REST-API that provides efficient retrieval of data from nanopore FAST5 data. This API has been connected with a front-end visualization extending Pileup.js and making use of Data Driven Documents (D3.js). Together the API and front-end enable a visualization platform for interactive analysis of nanopore signal data to confirm sequence base calls and this software is suitable for use in a mobile setting.

Matthew Links

Matthew Links

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