Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

By Chen-Shan Chin, David H. Alexander, Patrick J. Marks, Aaron A. Klammer, James P Drake, C. Heiner, Alicia Clum, Alex Copeland, J. Huddleston, Evan E. Eichler and 2 more. Nature Methods, 2013

3,955 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/effc7aeb714963389bd6672b696deb9b430ec0ca

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Citations in the corpus

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation (2017, positive): “All metagenomic assemblies in this study used the hierarchical genome-assembly process (HGAP3) 45 .”
Simultaneous Emergence of Multidrug-Resistant Candida auris on 3 Continents Confirmed by Whole-Genome Sequencing and Epidemiological Analyses (2017, methodology): “The reference genome was generated by de novo assembly of PacBio reads from isolate B8441, as described elsewhere [18], and used as a reference for single-nucleotide polymorphism (SNP) calling.”
Chloroplast genomes: diversity, evolution, and applications in genetic engineering (2016, background): “999 % can be achieved after such post-error corrections [46].”
Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage (2015, methodology): “One concern generated by the pre-polished assemblies was that their N50s were high, but their corrected N50s (23) after accounting for errors were low; however, Quiver and Pilon polishing dramatically improved the corrected N50s of the assemblies, indicating that the low corrected N50 values were du”
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome (2015, methodology): “The filtered set of alignments was then used to build a consensus using ‘pbdagcon’ (Chin et al. 2013) (https:// github.”
The Genome 10K Project: A Way Forward (2015, neutral): “Teleosts (30,195, 60) Sturgeons (26, 1) Paddlefish (2, 0)”
Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing (2016, methodology): “The FALCON assembler follows the design of the previous developed Hierarchical Genome Assembly Process (HGAP) 29 , although uses greatly optimized components for each step (Supplementary Figure 1) .”