PT  - JOURNAL ARTICLE
AU  - Yifei Xu
AU  - Kuiama Lewandowski
AU  - Sheila Lumley
AU  - Steven Pullan
AU  - Richard Vipond
AU  - Miles Carroll
AU  - Dona Foster
AU  - Philippa C Matthews
AU  - Timothy Peto
AU  - Derrick Crook
TI  - Detection of viral pathogens with multiplex Nanopore MinION sequencing: be careful with cross-talk
AID  - 10.1101/308262
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 308262
4099  - http://biorxiv.org/content/early/2018/04/25/308262.short
4100  - http://biorxiv.org/content/early/2018/04/25/308262.full
AB  - Metagenomic sequencing with the Oxford Nanopore MinION sequencer offers potential for point-of-care testing of infectious diseases in clinical settings. To improve cost-effectiveness, multiplexing of several, barcoded samples upon a single flow cell will be required during sequencing. We generated a unique sequencing dataset to assess the extent and source of cross barcode contamination caused by multiplex MinION sequencing. Sequencing libraries for three different viruses, including influenza A, dengue and chikungunya, were prepared separately and sequenced on individual flow cells. We also pooled the respective libraries and performed multiplex sequencing. We identified 0.056% of total reads in the multiplex sequencing data that were assigned to incorrect barcodes. Chimeric reads were the predominant source of this error. Our findings highlight the need for careful filtering of multiplex sequencing data before downstream analysis, and the trade-off between sensitivity and specificity that applies to the barcode demultiplexing methods.