GENOME ASSEMBLY

Advantages of long
reads for genome
assembly

WHITE PAPER October 2019

nanoporetech.com/publications nanoporetech.com
 Contents
De novo assembly 4

Advantages of long sequencing reads

for genome assembly 5
Ease of assembly 5
Facility to span repetitive genomic regions 5
Identification of large structural variation 6
Assembly quality 7

Genome assembly tools 8

Case studies 9
1. Assembling the human genome with
PromethION long reads 9
2. Genomic variation detection in disease 10
3. 100 tomato genomes in 100 days 11
4. Assembling the genome of an extremely
drug-resistant pathogen 12
5. Assembling metagenomes 13

Summary 14

About Oxford Nanopore Technologies 14

References 15

2
 Introduction
Over the last decade, improvements in next generation DNA sequencing
technology have transformed the field of genomics, making it an
essential tool in modern genetic and clinical research laboratories. The
facility to sequence whole genomes or specific genomic regions of
interest is delivering new insights into a variety of applications such as
human health and disease, metagenomics, antimicrobial resistance,
evolutionary biology, and crop breeding.

One of the key steps of WGS is the accurate assembly of the vast
amount of data generated into a contiguous stretch of DNA sequence.
This review provides a background to the DNA assembly process and
the associated advantages of long or ultra-long DNA reads, as provided
by nanopore sequencing technology.

For applications such as the analysis of larger

structural variation, or de novo assembly, whole-
genome sequencing (WGS) is typically the
technique of choice.

Whole-genome assembly — solving the puzzle

Traditional technologies have required users to sequence short lengths of DNA, which must
then be reassembled back into their original order as accurately as possible. Such short-read
sequencing technologies, however, present a number of challenges, particularly the difficulty
of accurately analysing repetitive regions and large structural variants1.

This means that many reference genomes that were created using short-read sequencing
are highly fragmented, which in turn introduces bias into any alignments made against that
reference2. This review shows how these challenges are now being met, by the emergence
of nanopore sequencing, which supports the generation of any length of sequencing read
— from short to ultra-long.

OXFORD NANOPORE TECHNOLOGIES | GENOME ASSEMBLY 3

 De novo assembly
De novo assembly aims to reconstruct the original genome sequence from the set of reads,
for example when there is no reference genome available or a researcher prefers to avoid
potential bias that could arise from using an imperfect reference. Generally, the first step is to
find overlaps between the reads and build a graph to describe their relationship.

Several approaches have been used for this purpose,

including Greedy extension, de Bruijn graphs, and Long sequencing reads support
Overlap Layout Consensus (OLC) (Figure 1). The graph simplified and less ambiguous
is then simplified and a consensus is extracted. A key genome assembly.
step in this process is the assembly of contiguous,
uninterrupted stretches of overlapping DNA, so-called
contigs. As detailed in the next section, long-read
capable sequencing technology offers many
advantages for both de novo and alignment-based
genome assembly.

Figure 1
A schematic showing how Long reads
long sequencing reads
can deliver simplified,
less ambiguous genome
assembly. Long reads (solid Short reads
arrows) have greater overlap
with other reads than is
provided by short reads
(dashed arrows), allowing
more accurate assemblies,
especially in repeat regions
(R). Image adapted from
Schatz (2014)3.

4
Advantages of long sequencing
reads for genome assembly
Until recently, cost-effective generation of large amounts of sequence data could only be
performed using short-read (<300 bp) sequencing technologies; however, nanopore-based
sequencing can process very long DNA fragments (current record >4 Mb)4 to create long
reads, which deliver a number of significant benefits.

Ease of assembly

The longer a sequencing read, the more overlap it will

have with other reads. As such, it is much easier to Long nanopore sequencing reads
assemble the DNA fragments back into the correct order. offer easier assembly and the ability
This can be visualised much like a jigsaw; the larger the to span repetitive genomic regions.
pieces, the easier the puzzle (Figure 2).

Facility to span repetitive genomic regions

Most genomes contain significant amounts of repetitive
DNA (e.g. transposons, satellites, gene duplications). As
the short reads produced by traditional next generation
sequencing (NGS) technology may not span each given
repetitive region, the resulting genome assemblies can
be highly fragmented2,5. Long-read capable sequencing
technologies have a significant advantage here as the
reads generated are more likely to span the full repetitive
region, allowing the creation of accurate genome
assemblies with minimal gaps (Figures 2 and 3).

Figure 2
Like a jigsaw puzzle with
large pieces, long-read DNA
is much easier to assemble
than short-read DNA. The
Escherichia coli genome
comprises 4.6 million bases,
which would equate to
92,000 fragments of 50 bp
or just 9 fragments of 500 kb
in length.

~ 50 base-pair read ~ 500,000 base-pair read

~ 92,000 “pieces” ~ 9 “pieces”

OXFORD NANOPORE TECHNOLOGIES | GENOME ASSEMBLY 5

 Genome sequence

Short reads

Short-read consensus

Long reads

Long-read consensus

Figure 3
A schematic highlighting the advantages of long reads in de novo assembly of repetitive regions.
Long read lengths are more likely to incorporate the whole repetitive region (blue boxes),
providing much simpler analysis and more accurate genome assemblies with fewer gaps.

Identification of large structural variation

The term structural variation (SV) covers a range of genetic

alterations, including copy number variation (CNV),
duplications, translocations, and inversions (Figure 4).
Traditionally, structural variants were defined as spanning
over 1,000 base pairs; however, with the advent of
higher-resolution techniques for genome analysis, this
definition has now been revised to include variants from
50 bp in length6. Structural variants have been
associated with a number of diseases, such as autism,
schizophrenia, and cancer; moreover, compared to
single nucleotide variants, they are 3 times as likely to be
associated with a genome-wide association signal6. It
has also been suggested that unknown SV may
contribute to the “missing heritability” of human disease6.
For these reasons, SV has become an increasingly
important area for research.
Most existing genome assemblies have been created
using short-read sequencing technology, which is limited
in its ability to capture large structural variation. Even the
well-studied human genome has large gaps in its
‘Structural variants…have been the
most difficult to characterize with the
use of short-read DNA sequencing
methods, and so pathogenic alleles
have gone undetected’6
assembly 7,8. As CNV alone is estimated to comprise
4.8–9.5% of the human genome9, it is clear that accurate
analysis of such regions is of significant importance.
Unlike short-read technology, longer nanopore
sequencing reads can cover the whole structural variant
in one read. This results in more accurate genome
assemblies, facilitating better understanding of genome
architecture in genetic diseases10.
For further details and sample-to-answer
guidance on genome assembly using Oxford
Nanopore long reads, view our Getting Started
guides at nanoporetech.com/resource-centre.

6
Figure 4
Structural variation a) classes and b) variant size and frequency in the human genome.
Image adapted from Huddleston (2017)11.

Assembly quality

The quality of genome assemblies is often assessed by
the number of contigs required to represent the genome,
the length of these contigs relative to the size of the
genome, and the proportion of reads that can be
assigned to the contigs. One of the most commonly
used assembly metrics is N50.
The contig N50 value is calculated by sorting all contigs
by length, calculating the cumulative assembly length (i.e.
adding the length of all contigs together), and identifying
the length of the contig which is situated in the middle of
the cumulative length (Figure 5). The higher the contig
N50 value, the more contiguous the assembly.
The much higher N50 values generated using long
nanopore sequencing reads underline the superior
quality and completeness of genome assembly when
compared with short-read sequencing technology.

N75 N50 N25

Figure 5
The N50 metric is one measure of the quality of a genome assembly. Other metrics such as
N75 and N25 are also sometimes used to further assess assembly quality. Image adapted from
Jansen (2016)12.

OXFORD NANOPORE TECHNOLOGIES | GENOME ASSEMBLY 7

 Genome assembly tools
A range of tools are available for genome assembly utilising long-read sequencing data
(Table 1). Tools differ in what they offer, and the extent of their use, and should be assessed
according to the specific project requirements. Assembly tools often include, or are coupled
with, error-correction methods (e.g. Racon13 and nanopolish14), which utilise information in the
assembled reads, or take information from other reads, to produce high consensus
accuracy.

A study by Cherukuri and Janga (2016) comparing a
number of assembly algorithms found the OLC approach
to be most favourable for nanopore long sequencing
reads — delivering higher genome coverage combined
with significantly larger average contig lengths, and lower
overall contig numbers15. However, other studies applying
combined de Bruijn and OLC approaches also report
accurate genome assemblies16,17. Researchers have also
compared long-read assembly tools for different
applications, such as in the context of human genome
assembly 8 and metagenomic analysis2.

Reference-guided/
Assembler Github link Reference
de novo

Canu De novo https://github.com/marbl/canu Koren et al. (2017)18

Flye De novo http://github.com/fenderglass/Flye Kolmogorov et al. (2019)19

Miniasm De novo https://github.com/lh3/miniasm Li (2016)20

RaGOO Reference-guided https://github.com/malonge/RaGOO Alonge et al. (2019)21

https://github.com/chanzuckerberg/
Shasta De novo Shafin et al. (2019)8
shasta

SMART https://github.com/ruanjue/
De novo Ruan22
denovo smartdenovo

Unicycler De novo https://github.com/rrwick/Unicycler Wick et al. (2017)23

Wtdbg2 De novo https://github.com/ruanjue/wtdbg2 Ruan and Li (2019)24

Table 1
Selection of assembly tools designed or adapted for Oxford Nanopore long reads.
For the latest genome assemblers, visit the Tools section of the Resource Centre at
www.nanoporetech.com/resource-centre.

8
CASE STUDY 1
Assembling the human genome
with PromethION long reads
Despite continual advancements in sequencing technology, full characterisation of the
human genome has yet to be achieved. Combining high output with the facility to generate
long and ultra-long reads, the PromethION platform from Oxford Nanopore Technologies
now makes de novo assembly of highly contiguous human genomes possible, both at scale
and with unprecedented efficiency.

Shafin and colleagues used an optimised PromethION
sequencing method and assembly workflow to
sequence 11 human cell lines in 9 days on a single
PromethION8. They obtained 2.3 Tb of sequence with an
average depth of coverage per sample of 63x and read
N50 of 42 kb, including 6.5x of “ultra-long” 100 kb+
reads (Figure 6).
‘…in terms of contemporary long-read
sequencing platforms, this throughput
is unmatched’8
The team introduced three new computational tools for
genome assembly and polishing: Shasta, a de novo
long-read assembler, and MarginPolish and HELEN, for
assembly polishing. Shasta was capable of producing a
draft human genome assembly in under 6 hours for only
$70 — a significant time and cost reduction compared to
the frequently-used Canu assembler. Using
MarginPolish/HELEN for polishing cost $108 and took 29
hours per sample, on average, and achieved 99.9%
sequence identity for haploid samples. The authors
stated that this could be even further improved by taking
advantage of the real-time capabilities of nanopore
sequencing: ’With real-time base calling, a DNA-to-de
novo assembly could be achieved in less than 96 hours
with little difficulty.’
The impact of comprehensive, rapid nanopore
sequencing workflows for human genetics is clear: ‘Such
speed could make these techniques practical for
screening human genomes for abnormalities in difficult-
to-sequence regions’ 8.

Figure 6
a) b) Nanopore sequencing
results: a) Read N50s
for each flow cell, and b)
genome depth of coverage
Coverage of a human genome (x)

(x) as a function of read

Read N50 (kb)

length. Dashed lines indicate

coverage at 10 kb and 100 kb.
HG00733 is presented in
bold as an example. Adapted
from Shafin (2019)8.

Read N50 (kb)

Individual genomes

OXFORD NANOPORE TECHNOLOGIES | GENOME ASSEMBLY 9

 CASE STUDY 2
Genomic variation
detection in disease
Obtaining highly contiguous genome assemblies with long nanopore sequencing reads
enables the comprehensive investigation of disease-associated variants.

Approximately 20–30% of lung cancer patients remain
undiagnosed with respect to their cancerous mutations;
variant detection is particularly pressing in cases where
an effective treatment remains elusive25. Using
PromethION whole-genome sequencing of cancer cell
lines and lung cancer specimens, Sakamoto et al.
identified a unique class of complex structural variant,
consisting of copy number changes, inversions, and
deletions, which could not be characterised using
short-read sequencing25. These variants were detected in
six of the nine clinical research specimens analysed, and
generally resulted in reduced gene expression levels and
disruption of genes in the region. The authors concluded
that these mutations may point to the causal mechanism
of disease in individuals for whom this is unknown.
Neuronal intranuclear inclusion disease (NIID) is a
progressive neurodegenerative disease which is difficult
to identify ante-mortem due to its wide range of clinical
manifestations; its genetic basis remains unsolved.
Through PromethION whole-genome sequencing of NIID
patients and their families, Jun Sone and colleagues
identified a repeat expansion within the gene
NOTCH2NLC which was consistently present in familial
and sporadic cases of the disease but absent from all
unaffected family members (Figure 7)26. Using the
Oxford Nanopore protocol for Cas9-mediated
enrichment, the team subsequently enriched for the
NOTCH2NLC repeat sequence to obtain higher read
coverage at this locus and form a consensus; the results
from this consensus analysis agreed well with their initial
analysis of the whole-genome sequencing data.

Figure 7
NOTCH2NLC repeat
consensus sequence of
multiple alignments. Note
that there are polymorphisms
between normal alleles. F1-1
and F2-2 are familial patients.
Expansion: allele with repeat
expansion; normal: normal
allele. Adapted from Sone
(2019)26.

10
CASE STUDY 3
100 tomato genomes
in 100 days
The tomato is one of the most valuable agricultural crops in the world, with an annual
production of over 175 million tonnes and a value of $85 billion. Tomatoes are also important
from a model system perspective due to their extensive phenotypic variation with over
15,000 known varieties27.

Michael Schatz and colleagues are sequencing 12–16

samples per week at 40x depth of coverage, using the
PromethION platform, to achieve a target of 100 genome
sequences in 100 days27. Initial results from the first 12
sequenced genomes revealed substantial variation
between samples, with between 25,000–45,000
structural variants per sample (Figure 8). For example,
an 83 kb tandem duplication was identified in the gene
EJ2; this was found to be associated with the higher fruit
yields observed in some plants28. The majority of
structural variants identified were sample-specific and
many had been missed using short-read sequencing,
which struggles to resolve large-scale genomic
differences.
‘Short-read sequencing has proven
valuable for single nucleotide
polymorphism discovery, but lacks
power for more complex structural
variants’ 27
Such large-scale sequencing efforts will enable the rapid
and high-throughput genome-wide characterisation of a
wide variety of tomato species, and potentially provide
the genetic information needed to enrich for desired
genome traits and increase the efficiency of crop
breeding in the future.

Figure 8
Nanopore sequencing results
from 12 tomato genomes a) b)
revealed (a) approximately
25,000–45,000 SVs per
genome, the majority of
which were deletions and
insertions, and (b) most
SVs were specific to each
sample. Figures courtesy of
Prof. Michael Schatz, Johns
Hopkins University, USA.

OXFORD NANOPORE TECHNOLOGIES | GENOME ASSEMBLY 11

 CASE STUDY 4
Assembling the genome
of an extremely
drug-resistant pathogen
Globally, with over 10 million new cases and 1.6 million deaths each year, and a growing
number of multi- and extremely-drug resistant strains, tuberculosis (TB) is a major threat to
human health29. Gaining a comprehensive understanding of genetic mechanisms
contributing to its transmission and resistance is therefore paramount for combatting drug-
resistant TB in endemic settings.

Short-read sequencing has been used for
Mycobacterium tuberculosis (MTB) assembly previously
yet it has limited ability to resolve long, repetitive regions
and structural variants, and is hindered by the relatively
high GC content (65%) of the MTB genome.
Using the Oxford Nanopore MinION, Bainomugisa et al.
performed whole-genome sequencing of the modern
Beijing lineage strain of TB responsible for drug
resistance outbreaks in the Western Province of Papua
New Guinea30. The team sequenced and assembled a
high-quality, complete genome, including all PE/PPE
(proline-glutamate/proline-proline-glutamate) gene
families, which are thought to contribute to virulence but
are often excluded from short-read sequencing analysis
due to their repetitive and GC-rich nature.
With a sequencing depth of 238x obtained from a single
MinION Flow Cell, a final assembly of 4,404,064 bp was
obtained in a single contig with >99.9% accuracy.
Furthermore, 166/168 PE/PPE genes had 100% breadth
of coverage at 299.87x depth, compared to a short-read
dataset of this strain where only 92/168 of these genes
obtained 100% coverage at an average depth of 46.3x.
Finally, genome-wide variant calling identified three
deleted genic regions and a 4,490 bp insertion that were
both absent from the H37RV reference strain genome
(Figure 9).

Figure 9
Integrative Genomic Viewer
(IGV) alignments of short-
read data from different
M. tuberculosis lineages
(A-G) mapped against the
nanopore draft genome. Left
image: a 4,490 bp insertion
spanning 7 annotated genes.
Right image: a 390 bp
insertion. Image courtesy
of Dr. Lachlan Coin, The
University of Queensland,
Australia.

12
CASE STUDY 5
Assembling metagenomes
Analysis of complex metagenomic samples has wide-reaching applications, with the
potential to recover genomes from previously unexplored microbial species, such as those
comprising gut microbiomes, as well as in the context of outbreak surveillance. Short-read
sequencing and assembly of metagenomes is challenging due to the difficulty in assigning
short reads to the correct genome of origin.

Bertrand and colleagues introduced the first hybrid

metagenome assembler, OPERA-MS31. Applying this tool
to the gut metagenomes from 28 antibiotic-treated
individuals, the team demonstrated that the integration of
long nanopore sequencing reads with short-read data
provided a 200-fold improvement in assembly contiguity
(Figure 10), and enabled completion of over 80 plasmid
or phage sequences. Such high-quality assemblies are
likely to provide a comprehensive insight into the gut
resistome.
In the context of outbreak surveillance, Liana
Kafetzopoulou and her team performed in-field
metagenomic sequencing and analysis during a major
Lassa fever virus (LASV) outbreak32. In 2018, the Nigerian
Lassa fever season experienced the largest ever upsurge
in cases, raising fears of an emergent strain with increased
transmission rate. The LASV genome is highly variable and
therefore, for genome analysis, an unbiased metagenomic
approach is preferable to targeted amplicon or capture-
based whole-genome sequencing methods.
Benefiting from the speed and portability of real-time
sequencing with the MinION, the team sequenced 120
infected human samples over 7 weeks at the epicentre of
‘Portable metagenomic sequencing
of genetically diverse RNA viruses on
the MinION…and with no pathogen-
specific enrichment, is shown to be
a feasible methodology enabling a
real-time characterization of potential
outbreaks in the field’32
the outbreak. An average of 4.26% of the sequencing
reads were LASV, which was sufficient for phylogenetic
comparison of at least one genomic segment in 91/120
samples tested. Hepatitis A virus co-infection was also
detected in one sample, comprising 0.1% of reads which
provided 74% genome coverage and 20x depth, using
the Centrifuge metagenomic classification software. This
demonstrated the potential of their simple approach for
identifying multiple RNA viruses, even within the same
sample. They identified that rodent hosts were the main
source of the upsurge in cases, as opposed to person-
to-person transmission, with no strong evidence of a
new emerging strain. The results were immediately
reported to the WHO and Nigerian authorities,
supporting a rapid public health response to the
outbreak.

Figure 10
Increase in assembly
contiguity as a function
of read coverage for a
representative short-read
assembler (a), long-read
assembler (b), and the hybrid
OPERA-MS assembler (c).
Unassembled genomes
are shown as circles with
black borders. Adapted from
Bertrand (2019)31.

OXFORD NANOPORE TECHNOLOGIES | GENOME ASSEMBLY 13

 Summary
Oxford Nanopore sequencing technology, which is capable of generating ultra-long reads
in excess of 4 Mb4, offers a real solution to the challenges associated with genome
assembly, such as accurately sequencing and mapping repetitive sequences and
structural variants, improving the completeness of genome assemblies where short-read
sequencing has failed6,7,10,30. Long nanopore sequencing reads offer unique potential for
genome assembly across a range of applications, from human and plant disease research
to bacterial metagenomics.

It is clear that the growing usage of Oxford Nanopore sequencing technology and
associated improvements in genome assemblies will bring additional and rapid insight
into genomics, further refining the relationship of phenotype to genotype.

About Oxford
Nanopore Technologies
Oxford Nanopore Technologies introduced the world’s
first nanopore DNA sequencer, the MinION — a portable,
real-time, low-cost device — followed by the larger
GridION, PromethION P24 and P48 devices, and smaller
Flongle (Figure 11). The latest addition to the range,
MinION Mk1C, combines the portability and power of the
MinION with high-performance compute and an
integrated touchscreen, providing a complete, go-
anywhere solution for nanopore sequencing.
Enabling the generation of long sequencing reads,
Oxford Nanopore platforms deliver high-quality whole-
genome sequencing with the facility to span repetitive
regions and structural variants, offering significant
advantages over traditional short-read sequencing
technology.
A number of protocols are available for nanopore
sequencing, enabling optimised whole-genome analysis
for a range of sample types and DNA input amounts. Our
dedicated whole-genome sequencing Getting Started
guides, available on the Resource centre (nanoporetech.
com/resource-centre), have been developed to provide
further details and sample-to-answer guidance on
genome assembly with Oxford Nanopore long reads.
Find out more at: www.nanoporetech.com

Figure 11
Oxford Nanopore sequencing platforms (from left to right): Flongle, a flow cell adapter for MinION and GridION; the portable
MinION and the latest addition, MinION Mk1C; GridION, with capacity for five Flongle or MinION Flow Cells; and the high-
throughput PromethION (P24 or P48) platform.

14
References
1. Mak, A. C. et al. Genome-Wide
structural variation detection by
genome mapping on nanochannel
arrays. Genetics 202(1):351–62 (2016).
2. Latorre-Perez, A. et al. Assembly
methods for nanopore-based
metagenomic sequencing: a
comparative study. BioRxiv 722405
(2019).
3. Schatz, M. De novo assembly of
complex genomes using single
molecule sequencing. Presentation.
Available at: http://schatzlab.cshl.
edu/presentations/2014-01-14.PAG.
Single%20Molecule%20Assembly.pdf
[Accessed: 3 October 2019]
4. Oxford Nanopore Technologies. Ultra-
Long DNA Sequencing Kit. Available
at: https://store.nanoporetech.com/
ultra-long-dna-sequencing-kit.html
[Accessed: 23 August 2021]
5. Chaisson, M. J. P. et al. Genetic
variation and the de novo assembly
of human genomes. Nat. Rev. Genet.
16(11):627–40 (2015).
6. Eichler, E. Genetic Variation,
Comparative Genomics, and the
Diagnosis of Disease. N. Engl. J. Med.
381:64-74 (2019).
7. Miga, K. Telomere-to-telomere
assembly of a complete human X
chromosome. Presentation. Available
at: https://nanoporetech.com/
resource-centre/telomere-telomere-
assembly-complete-human-x-
chromosome [Accessed: 9 September
2019]
8. Shafin, K. et al. Efficient de novo
assembly of eleven human genomes
using PromethION sequencing and a
novel nanopore toolkit. BioRxiv 715722
(2019)
9. Zarrei, M. et al. A copy number
variation map of the human genome.
Nat. Rev. Genet. 16(3):172–83 (2015).
10. Ebbert, M. T. W. et al. Systematic
analysis of dark and camouflaged
genes reveals disease-relevant genes
hiding in plain sight. Genome Biol.
20(1):97 (2019).
11. Huddleston, J. et al. Discovery and
genotyping of structural variation from
long-read haploid genome sequence
data. Genome Res. 27(5): 677-685
(2017).
OXFORD NANOPORE TECHNOLOGIES | GENOME ASSEMBLY
12. Jansen, H. De novo genome assembly
with MinION long reads. Presentation.
Available at: https://community.
nanoporetech.com/posts/136
[Accessed: 30 September 2019]
13. Sovic, I. et al. Github: Racon [Online].
Available at: https://github.com/lbcb-
sci/racon [Accessed: 9 September
2019]
14. Simpson, J. Github: Nanopolish
[Online]. Available at: https://github.
com/jts/nanopolish [Accessed: 9
September 2019]
15. Cherukuri, Y. and Janga, S. C.
Benchmarking of de novo assembly
algorithms for Nanopore data
reveals optimal performance of OLC
approaches. BMC Genomics 22:17
Suppl 7:507 (2016).
16. Lin, Y. et al. Assembly of long
error-prone reads using de Bruijn
graphs. Proc. Natl. Acad. Sci. USA
113(52):E8396-E8405 (2016).
17. Judge, K. et al. Comparison
of bacterial genome assembly
software for MinION data and their
applicability to medical microbiology.
Microbial Genomics doi: 10.1099/
mgen.0.000085 (2016).
18. Koren, S. et al. Canu: scalable and
accurate long-read assembly via
adaptive k-mer weighting and repeat
separation. Genome Res. 27:722-736
(2017).
19. Kolmogorov, M. et al. Assembly of
long, error-prone reads using repeat
graphs. Nat. Biotech. 37:540-546
(2019).
20. Li, H. Minimap and miniasm: fast
mapping and de novo assembly for
noisy long sequences. Bioinformatics
32:2103–10 (2016).
21. Alonge, M. et al. Fast and accurate
reference-guided scaffolding of draft
genomes. BioRxiv 519637 (2019).
22. Ruan, J. Available at: https://github.
com/ruanjue/smartdenovo [Accessed:
5 January 2017].
23. Wick, R. R. et al. Unicycler: Resolving
bacterial genome assemblies from
short and long sequencing reads.
PLoS Comput. Biol. 13(6): e1005595
(2017).
24. Ruan, J. and Li, H. Fast and accurate
long-read assembly with wtdbg2.
BioRxiv 530972 (2019).
25. Sakamoto, Y. et al Long read
sequencing reveals a novel class of
structural aberrations in cancers:
identification and characterization of
cancerous local amplifications. BioRxiv
620047 (2019).
26. Sone, J. et al. Long-read sequencing
identifies GGC repeat expansions in
NOTCH2NLC associated with neuronal
intranuclear inclusion disease. Nat.
Genet. 51(8):1215-1221 (2019).
27. Schatz. M. 100 genomes in 100 days:
The structural variant landscape in
tomato genomes. Available at: https://
nanoporetech.com/resourcecentre/
michael-schatz-100-genomes-100-
days-structural-variantlandscape-
tomato-genomes [Accessed: 7 May
2019]
28. Soyk, S et al. Duplication of a
domestication locus neutralized a
cryptic variant that caused a breeding
barrier in tomato. Nat. Plants. 5(5):471-
479 (2019).
29. WHO (2018) Tuberculosis [Online].
Available at: https://www.who.int/
en/news-room/fact-sheets/detail/
tuberculosis [Accessed: 17 September
2019]
30. Bainomugisa, A. et al. A complete
high-quality MinION nanopore
assembly of an extensively drug-
resistant Mycobacterium tuberculosis
Beijing lineage strain identifies novel
variation in repetitive PE/PPE gene
regions. Microb. Genom. doi: 10.1099/
mgen.0.000188 (2018).
31. Bertrand, D. et al. Hybrid metagenomic
assembly enables high-resolution
analysis of resistance determinants
and mobile elements in human
microbiomes. Nat. Biotechnol.
37(8):937-944 (2019).
32. Kafetzopoulou, L. E. et al. Metagenomic
sequencing at the epicenter of the
Nigeria 2018 Lassa fever outbreak.
Science 363(6422):74-77(2019).
15
Oxford Nanopore Technologies
phone +44 (0)845 034 7900
email sales@nanoporetech.com
twitter @nanopore
www.nanoporetech.com

Oxford Nanopore Technologies, the Wheel icon, Flongle, GridION, MinION, PromethION, and VolTRAX are registered
trademarks of Oxford Nanopore Technologies in various countries. All other brands and names contained are the property of
their respective owners. © 2021 Oxford Nanopore Technologies. All rights reserved. Flongle, GridION, MinION, PromethION,
and VolTRAX are for research use only.

WP_1043(EN)_V3_24Aug2021