2017
DOI: 10.12688/f1000research.10545.1
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Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis

Abstract: Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novo assembled a single contig mitochondrial genome from N. brasiliensi… Show more

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Cited by 15 publications
(18 citation statements)
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“…One of the most recent sequencing technologies available on the market is the MinION sequencing device from Oxford Nanopore Technologies (ONT) 2 . A brief overview of MinION sequencing technology is discussed in our previous study on mitochondrial genome assembly 3 .…”
Section: Introductionmentioning
confidence: 99%
“…One of the most recent sequencing technologies available on the market is the MinION sequencing device from Oxford Nanopore Technologies (ONT) 2 . A brief overview of MinION sequencing technology is discussed in our previous study on mitochondrial genome assembly 3 .…”
Section: Introductionmentioning
confidence: 99%
“…The N. brasiliensis strain used in this study was originally sourced from Lindsey Dent (University of Adelaide) and maintained at the Malaghan Institute for 22 years by serial passage through female Lewis rats [ 31 ]. Ethics approval is overseen and approved by the Animal Ethics Committee of Victoria University of Wellington.…”
Section: Methodsmentioning
confidence: 99%
“…Five samples of 25 mg each of frozen worms, cultured, harvested and purified as previously described [ 31 ], were sent to Simon Mayes (ONT) and subject to different methods of sample preparation (see Additional file 4 : Table S2): Sonication, DNeasy: Worms were disrupted by sonication and then processed using a Qiagen DNeasy kit (ATL/AL, 30 min at 56 °C). This yielded 900 ng of DNA and 1800 ng of RNA.…”
Section: Methodsmentioning
confidence: 99%
“…In this context, the portability and reduced costs of sequencing with the MinION device (Oxford Nanopore Technologies) has facilitated the adoption of this technology in many distinct applications[16]. Besides its utility for the analysis of structural variants[17,18], SNP determination[19], cytosine methylation[20], transcriptomics[21], and in-field experiments in extreme environments[22], MinION has widely used to sequence small whole genomes from virus (10.8 kb)[23], mitochondrial DNA (16 kb)[24], and bacteria (4.6 Mb)[25], allowing their assembly into single contigs when depth of coverages were above 20–40X[26]. Nevertheless, this technology continues to be challenged by its high error rate (>10%)[27], particularly in homopolymeric regions[28], and the generation of reads that fail to align against the target[29,30].…”
Section: Introductionmentioning
confidence: 99%
“…Nevertheless, this technology continues to be challenged by its high error rate (>10%)[27], particularly in homopolymeric regions[28], and the generation of reads that fail to align against the target[29,30]. Because of this, hybrid assemblies leveraging the per-base quality of high-coverage (>200X) second-generation data with the bridging capacity of >10X depth-of-coverage third-generation data is nowadays perceived as the optimal choice for obtaining accurate assemblies[24,27,3135]. Given the large variability in sequence throughput offered by this technology well below product specifications, here we tested the benefit of shallow MinION sequencing data in assisting the hybrid genome assembly of a S. agalactiae clinical isolate (genome size of 2.2 Mb).…”
Section: Introductionmentioning
confidence: 99%