Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage

By M. Chakraborty, James G. Baldwin-Brown, Anthony D. Long, J. Emerson. bioRxiv, 2015

439 citations recorded by the source corpus.

Genome assemblies that are accurate, complete, and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements, and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a “missing manual” that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/687c6718528e0240f9c9db612e3de44c39fe3b99

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Citations in the corpus

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation (2016, background): “Previously, at least 50× coverage was recommended for hierarchical assembly methods (Berlin et al. 2015; Chakraborty et al. 2016).”
Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, positive): “A comparison to other patching tools showed that RagTag “patch” outperformed DENTIST [20] and it was competitive with SAMBA [21] and Quickmerge [22] (Additional file 2: Table S4).”