GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
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Summary
A practical implementation of the polyploid-aware mixture model that quickly and accurately infers genome properties across thousands of simulated and several real datasets spanning a broad range of complexity is described and evaluated.
- Type
- article
- Published
- 2020-03-18
- Cited by
- 2,437
- References
- 40
- Access
- Open access
- OpenAlex
- https://openalex.org/W3012094285
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:202027276
Keywords
Polyploid, Genome, Ploidy, Loss of heterozygosity, Biology
References
- T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
- A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
- The evolutionary consequences of polyploidy.
- Why Assembling Plant Genome Sequences Is So Challenging
- HYBRID ORIGIN OF POLYPLOIDY IN FRESHWATER SNAILS OF THE GENUS BULINUS (MOLLUSCA: PLANORBIDAE)
- Doubling down on genomes: polyploidy and crop plants.
- A fast, lock-free approach for efficient parallel counting of occurrences of k-mers
- Polyploidy in fishes: patterns and processes
- Informed and automated k-mer size selection for genome assembly
- Allotetraploid and autotetraploid models of linkage analysis
- Quake: quality-aware detection and correction of sequencing errors
- Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita
- KmerStream: Streaming algorithms for k-mer abundance estimation
- Exploring genome characteristics and sequence quality without a reference
- ON THE ABUNDANCE OF POLYPLOIDS IN FLOWERING PLANTS
- Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum[OPEN]
- THE DIPLOID‐LIKE CYTOLOGICAL BEHAVIOR OF TETRAPLOID COTTON
- Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers
- Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing
- KMC 3: counting and manipulating k‐mer statistics
Cited by
- Genomic features of asexual animals
- Mapping-based genome size estimation
- Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)
- Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat
- Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)
- High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing
- Rooibos (Aspalathus linearis) Genome Size Estimation Using Flow Cytometry and K-Mer Analyses
- Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms
- Genome assembly of six polyploid potato genomes
- Genome sequence of the root-knot nematode Meloidogyne luci
- Highly accurate long-read HiFi sequencing data for five complex genomes
- Maintenance of Species Differences in Closely Related Tetraploid Parasitic Euphrasia (Orobanchaceae) on an Isolated Island
- Mycena genomes resolve the evolution of fungal bioluminescence
- Conservative route to genome compaction in a miniature annelid
- Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies
- The gene-rich genome of the scallop Pecten maximus
- Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes.
- Whole-genome, transcriptome, and methylome analyses provide insights into the evolution of platycoside biosynthesis in Platycodon grandiflorus, a medicinal plant
- The Genome Sequence of the Octocoral Paramuricea clavata – A Key Resource To Study the Impact of Climate Change in the Mediterranean
- Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium
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