Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly pipeline
By F. Bakker, Diya Lei, Jiaying Yu, S. Mohammadin, Zhen Wei, Sara J. van de Kerke, B. Gravendeel, Mathijs Nieuwenhuis, M. Staats, D. E. Alquezar‐Planas and 1 more. 2016
137 citations recorded by the source corpus.
Subfields: Cell Biology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/9c6eb376dd69c4f0f8c136d0669199b24694a524
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In Molecular Biology
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Citations in the corpus
- OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes (2019, background): “There are many assembly methods and pipelines [e.g., GetOrganelle or IOGA; (4,5)], and we are currently aware of no less than twelve (semi-)automatic annotation tools for organellar genomes (1,3,6-15).”
- BlobToolKit – Interactive Quality Assessment of Genome Assemblies (2019, background): “Organelles will usually have high coverage relative to the nuclear genome (Bakker et al. 2016) and collapsed segmental duplications in the assembly will also have elevated coverage (Bailey et al. 2002).”
- Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae (2021, methodology): “Contrasting to RADseq and RNAseq method, the DGS method can effectively utilize degraded DNA from herbarium specimens of rare, extinct, or ancient samples, which has been well tested in recent studies (Särkinen et al., 2012; Bakker et al., 2016; Saeidi et al., 2018; Liu et al., 2019, 2020a).”
- GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes (2018, methodology): “It starts with recruitment of initial target-associated reads by using Bowtie2 and taking target genome(s) or sequence(s) as the seed; the initial target-associated reads (seed-mapped reads) are treated as “ baits ” to get more target-associated reads through multiple extension iterations, which is ”