Oxford-Nanopore eBook - 7

SEQUENCING: generating high
yields on the PromethION

Find out more about PromethION:
nanoporetech.com/products/promethion

Bases sequenced

unfragmented

SRE + MRIII*

g-TUBE
0

100

Read length (kb)

For a human whole-genome survey, generating sufficient data
for ~30x depth of coverage is a good starting point; this can be
obtained by sequencing on a single PromethION Flow Cell for
72 hrs. Throughput is maximised by a nuclease flush and addition
of fresh library every 24 hrs. For best metrics, we recommend
upping this depth to >45x, or for a more cost-effective,
light-touch approach, this could be lowered to 15x.

The PromethION is available configured for 24 or 48 individuallyaddressable flow cells, leaving the rest of the device free for other
experiments to be started and stopped as needed. Basecalling
can be carried out in real-time on the device, making use of the
powerful onboard compute.
*Circulomics Short Read Eliminator Kit + Diagenode Megaruptor 3

Find out more about nanopore sequencing service providers: nanoporetech.com/services/providers

ANALYSIS: calling SVs without
command line

Find out more about data analysis solutions:
nanoporetech.com/nanopore-sequencing-data-analysis

To call variants in your long-read data, we recommend
pipeline-structural-variation, available on github. The
pipeline takes the FASTQ files produced by onboard
basecalling, aligns to a provided FASTA reference
genome, calls insertions, deletions and duplications
>50 bp and outputs a VCF file and QC report. Our SV
pipeline tutorial provides step-by-step instructions for
the full process, including visualisation. View the tutorial
here: community.nanoporetech.com/knowledge/
bioinformatics
For those wishing to avoid command line, our cloudbased EPI2ME™ SV workflow provides fully automated
human whole-genome SV analysis based on the same
pipeline, generating a VCF file.

FASTQ input file
QC & filter reads

Align reads

minimap2

Call variants

sniffles

Filter variants

VCF output file

Find out more at: nanoporetech.com/applications/structural-variation

References:
1. E. E. Eichler, 2019. NEJM. DOI: 10.1056/NEJMra1809315
2. M. T. W. Ebbert et al. 2019. Genome Biol. DOI: 10.1186/s13059-019-1707-2

Twitter: @nanopore
www.nanoporetech.com

Oxford Nanopore Technologies, the wheel icon, EPI2ME and PromethION are registered trademarks
of Oxford Nanopore Technologies in various countries. All other brands and names contained are the
property of their respective owners. © 2019 Oxford Nanopore Technologies.
Oxford Nanopore Technologies products are currently for research use only. WF_1042(EN)_V1_01Oct2019

http://www.nanoporetech.com/products/promethion http://www.nanoporetech.com/services/providers http://www.nanoporetech.com/nanopore-sequencing-data-analysis http://community.nanoporetech.com/knowledge/bioinformatics http://community.nanoporetech.com/knowledge/bioinformatics http://www.nanoporetech.com/applications/structural-variation http://www.nanoporetech.com

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