Oxford-Nanopore eBook - 15

Impact
This study produced a high-quality, fully annotated XDR-TB genome assembly
with potential for use as a reference genome in future outbreak surveillance.
Characterisation of SNPs, indels and structural variants provided insights into
the genetics underpinning the phenotype of this pathogen.

Results
Assembly produced a single contig, allowing full resolution of structural
variants and the identification of novel SNPs in the GC-rich, highly
repetitive PE/PPE genes implicated in pathogenicity and virulence.

238x
depth of coverage
of genome

4.4 Gbp 99.92% 166/168 4.4 kbp
single-contig
assembly

HOW?
DNA from a Beijing-lineage XDR-TB
strain from Western Province, Papua
New Guinea was sequenced on one
MinION Flow Cell. Hybrid assembly
was performed, followed by analysis
of SNPs, indels and structural variants
in the genome.

de novo nanopore
assembly accuracy

Kit

PE/PPE genes
assembled

insertion
identified

Oxford Nanopore Ligation Sequencing Kit

Available here: store.nanoporetech.com/ligation-sequencing-kit.html

Device

MinION

Tools

Custom analysis pipeline, including:
- Canu (de novo assembly)
- Nanopolish (polishing and SNP/indel calling)
- Racon (error correction with raw nanopore reads)
- Pilon (short read error correction)

Find out more about analysis pipelines available here:
community.nanoporetech.com/knowledge/bioinformatics

Find out more at: nanoporetech.com/applications/whole-genome-sequencing
Publication
A. Bainomugisa 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. Microbial Genomics (2018). DOI: https://dx.doi.org/10.1099/mgen.0.000188

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© 2019 Oxford Nanopore Technologies.

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RS_1032(EN)_V1_17Jun2019

http://store.nanoporetech.com/ligation-sequencing-kit.html http://community.nanoporetech.com/knowledge/bioinformatics http://www.nanoporetech.com/applications/whole-genome-sequencing https://dx.doi.org/10.1099/mgen.0.000188 http://www.nanoporetech.com

Oxford-Nanopore eBook

Table of Contents for the Digital Edition of Oxford-Nanopore eBook