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
Oxford Nanopore Technologies, the Wheel icon and MinION are registered
trademarks of Oxford Nanopore Technologies in various countries.
© 2019 Oxford Nanopore Technologies.
Twitter: @nanopore
www.nanoporetech.com
Oxford Nanopore Technologies products are currently for research use only.
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
Contents
Oxford-Nanopore eBook - 1
Oxford-Nanopore eBook - 2
Oxford-Nanopore eBook - Contents
Oxford-Nanopore eBook - 4
Oxford-Nanopore eBook - 5
Oxford-Nanopore eBook - 6
Oxford-Nanopore eBook - 7
Oxford-Nanopore eBook - 8
Oxford-Nanopore eBook - 9
Oxford-Nanopore eBook - 10
Oxford-Nanopore eBook - 11
Oxford-Nanopore eBook - 12
Oxford-Nanopore eBook - 13
Oxford-Nanopore eBook - 14
Oxford-Nanopore eBook - 15
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Oxford-Nanopore eBook - 19
Oxford-Nanopore eBook - 20
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