A complete bacterial genome assembled de novo using only nanopore sequencing data

By Nicholas J. Loman, Joshua Quick, Jared T. Simpson. Nature Methods, 2015

1,217 citations recorded by the source corpus.

We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data. Our method has three stages: (i) overlaps are detected between reads and then corrected by a multiple-alignment process; (ii) corrected reads are assembled using the Celera Assembler; and (iii) the assembly is polished using a probabilistic model of the signal-level data. The assembly reconstructs gene order and has 99.5% nucleotide identity.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/272863dd9a13bfdbf5ac0c41418702959eb654fc

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Nanopore sequencing technology, bioinformatics and applications (2021, methodology): “In addition to the genome-polishing software Nanopolish 109 , ONT released Medaka, a neural network-based method, aiming for improved accuracy and speed compared to Nanopolish (Table 1).”
Long-read human genome sequencing and its applications (2020, neutral): “Most of these errors can be resolved with use of polishing tools (such as Racon 48 , Nanopolish 63,85,86 , MarginPolish 36 , HELEN 36 , Quiver 46 , Arrow and Medaka) and error correction with short-read sequence data generated from the same individual 47 .”
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies (2018, background): “Recent advances in third-generation single-molecule sequencing have enabled de novo genome assemblies that have extremely high levels of contiguity and completeness [1 – 3].”
Falco: high-speed FastQC emulation for quality control of sequencing data (2019, neutral): “High-throughput sequencing is routinely used to profile copy number variations in cancers 1 , assemble genomes of microbial organisms 2,3 , quantify gene expression 4 , identify cell populations from single-cell transcriptomes in a variety of tissues 5 and track epigenetic changes in developing…”
Piercing the dark matter: bioinformatics of long-range sequencing and mapping (2018, methodology): “These include Quiver 36 or Arrow for PacBio (see Related links), Nanopolish 46 for Oxford Nanopore or Pilon for polishing long-read assemblies with additional Illumina reads 47 .”
MinION Analysis and Reference Consortium: Phase 1 data release and analysis (2015, methodology): “…al ., 2015; Ashton et al. , 2015; Greninger et al ., 2015; Jain et al., 2015; Karlsson et al ., 2015; Kilianski et al ., 2015; Laver et al ., 2015; Loman et al ., 2015; Mulley & Hargreaves, 2015; Quick et al ., 2014; Urban et al., 2015; Wang et al. , 2015) and these provided a first glimpse of…”
Completing bacterial genome assemblies with multiplex MinION sequencing (2017, methodology): “0) to calculate consensus base calls using signal-level analysis (based on the fast5 files) [12].”
Current challenges and best-practice protocols for microbiome analysis (2019, background): “At present, MinION provides >10 Gbp yield per flow cell with >10 times longer read coverage of even low abundant genomes (<1%) [151, 152].”
Transcriptomics technologies (2017, methodology): “Direct sequencing of RNA using nanopore sequencing represents a current state-of-the-art RNA-Seq technique in its infancy (in prerelease beta testing as of 2016) [77][78].”
De novo assembly of haplotype-resolved genomes with trio binning (2018, positive): “For example, the partitioned read sets can be reused for haplotype-specific gap filling 45 and consensus polishing 46, 47 , and we have shown that polishing with haplotype-specific reads achieves a more accurate consensus sequence.”
Oxford Nanopore MinION Sequencing and Genome Assembly (2016, methodology): “However, most of the missing homopolymers can be recovered from the event data by Nanopolish [17].”
Detecting DNA cytosine methylation using nanopore sequencing (2017, methodology): “The transition probabilities are as previously described [1].”
Mash: fast genome and metagenome distance estimation using MinHash (2015, background): “coli 1D MinION reads [29], which had an average sequencing error rate of ~40%.”
Computational pan-genomics: status, promises and challenges (2016, background): “New long-read technologies (e.g. PacBio, Oxford Nanopore) are now providing the first promising results in the sequencing of complete viral genomes [40, 41].”