One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

By Sergey Koren, Adam M. Phillippy. Current Opinion in Microbiology, 2015

402 citations recorded by the source corpus.

Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality) genomes. In contrast, emerging long-read sequencing technologies can now produce reads tens of kilobases in length, enabling the automated finishing of microbial genomes for under $1000. This promises to improve the quality of reference databases and facilitate new studies of chromosomal structure and variation. We present an overview of these new technologies and the methods used to assemble long reads into complete genomes.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c49b4c08364d620cd084d9d0f46c5a1cd815db94

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Citations in the corpus

PacBio Sequencing and Its Applications (2015, methodology): “For microbial genomes, 100 coverage is reliable for resolving repetitive regions and costs less than $1000 with a 20 kb library preparation [6].”
Third generation sequencing: technology and its potential impact on evolutionary biodiversity research (2016, background): “Assembling genomes solely based on short reads without any available reference genome remains a challenge (Koren & Phillippy, 2015).”
Polypolish: Short-read polishing of long-read bacterial genome assemblies (2021, neutral): “For bacterial genomes, reads from these platforms are often longer than the largest repeat in the genome, making complete assemblies (one contig per replicon) possible [1].”
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads (2020, background): “Recently, long-read sequencing technologies have significantly simplified assembly by generating multikilobase reads, which span most common genomic repeats (Chin et al. 2013; Koren et al. 2013; Koren and Phillippy 2014; Gordon et al. 2016; Bickhart et al. 2017; Kronenberg et al. 2018).”
A review of methods and databases for metagenomic classification and assembly (2019, background): “MetaQUAST [128] computes genome statistics of metagenomics assemblies, and, by aligning against reference genomes, can report the number of”
Current challenges and best-practice protocols for microbiome analysis (2019, methodology): “In this context, third-generation sequencing platforms like Pacific Biosciences RS II/Sequel and Oxford Nanopore MinION sequencing technologies prove to be more efficient due to longer read sizes, species-level resolution and absence of DNA amplification-based biases [59, 60].”
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage (2015, neutral): “PacBio only methods, which typically require higher coverage (5)).”
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016, background): “Several new approaches have been developed to address this, roughly categorized as hybrid, hierarchical, or direct (for a review, see Koren and Phillippy 2014).”
Big Data: Astronomical or Genomical? (2015, background): “Though error rates currently are higher and throughput lower than short-read technologies, as they mature, these technologies are starting to be used to sequence and assemble nearly entire chromosomes [29].”
Assembly of long error-prone reads using de Bruijn graphs (2016, background): “Advances in assembly and mapping of long error-prone reads recently resulted in accurate assemblies of various genomes [28, 29, 31], reconstruction of complex regions of the human genome [15, 22], and resolving complex tandem repeats [60].”
Circlator: automated circularization of genome assemblies using long sequencing reads (2015, background): “Cambridge, UK Nanopore Technologies (ONT), has again improved the contiguity of automated de novo assemblies to the point where production of a single contig per DNA molecule is now possible on an unprecedented scale for bacterial and small eukaryotic genomes [2].”