Estimating the k-mer Coverage Frequencies in Genomic Datasets: A Comparative Assessment of the State-of-the-art

Manekar, Swati; Sathe, S. R.

doi:10.2174/1389202919666181026101326

Cited by 13 publications

(12 citation statements)

References 41 publications

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“…The overall genome duplication level in H. meleagridis was computed directly as the fraction of the genome that is duplicated instead of inferring this figure by indirect methods (i.e. [ 14 ]). To calculate this, we aligned the contigs to themselves with nucmer and extracted homologous regions with the show-coords tool [ 15 ].…”

Section: Resultsmentioning

confidence: 99%

Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

et al. 2021

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Background Histomonas meleagridis is a protozoan parasite and the causative agent of histomonosis, an important poultry disease whose significance is underlined by the absence of any treatment and prophylaxis. The recent successful in vitro attenuation of the parasite urges questions about the underlying mechanisms. Results Whole genome sequence data from a virulent and an attenuated strain originating from the same parental lineage of H. meleagridis were recruited using Oxford Nanopore Technology (ONT) and Illumina platforms, which were combined to generate megabase-sized contigs with high base-level accuracy. Inspecting the genomes for differences identified two substantial deletions within a coding sequence of the attenuated strain. Additionally, one single nucleotide polymorphism (SNP) and indel targeting coding sequences caused the formation of premature stop codons, which resulted in the truncation of two genes in the attenuated strain. Furthermore, the genome of H. meleagridis was used for characterizing protein classes of clinical relevance for parasitic protists. The comparative analysis with the genomes of Trichomonas vaginalis, Tritrichomonas foetus and Entamoeba histolytica identified ~ 2700 lineage-specific gene losses and 9 gene family expansions in the H. meleagridis lineage. Conclusions Taken as a whole, the obtained data provide the first hints to understand the molecular basis of attenuation in H. meleagridis and constitute a genomics platform for future research on this important poultry pathogen.

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Section: Resultsmentioning

confidence: 99%

Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

et al. 2021

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“…Briefly, k‐mers are sequences of length “k” contained within the genome assembly and k‐mer profiles provide estimates of data quality, completeness, and complexity (Simpson, 2014). There are several programs available for k‐mer analyses with trade‐offs between speed, accuracy, and memory usage for analyses (Manekar & Sathe, 2019; Mapleson et al, 2017; Vurture et al, 2017). These k‐mer profiles provide critical information regarding genome assemblies and may also identify mis‐assembly problems such as repeated sequences that have been inappropriately collapsed.…”

Section: Evaluating Assembliesmentioning

confidence: 99%

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Whibley

Kelley

Narum

2021

Molecular Ecology Resources

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The quality of genome assemblies has improved rapidly in recent years due to continual advances in sequencing technology, assembly approaches, and quality control. In the field of molecular ecology, this has led to the development of exceptional quality genome assemblies that will be important long‐term resources for broader studies into ecological, conservation, evolutionary, and population genomics of naturally occurring species. Moreover, the extent to which a single reference genome represents the diversity within a species varies: pan‐genomes will become increasingly important ecological genomics resources, particularly in systems found to have considerable presence‐absence variation in their functional content. Here, we highlight advances in technology that have raised the bar for genome assembly and provide guidance on standards to achieve exceptional quality reference genomes. Key recommendations include the following: (a) Genome assemblies should include long‐read sequencing except in rare cases where it is effectively impossible to acquire adequately preserved samples needed for high molecular weight DNA standards. (b) At least one scaffolding approach should be included with genome assembly such as Hi‐C or optical mapping. (c) Genome assemblies should be carefully evaluated, this may involve utilising short read data for genome polishing, error correction, k‐mer analyses, and estimating the percent of reads that map back to an assembly. Finally, a genome assembly is most valuable if all data and methods are made publicly available and the utility of a genome for further studies is verified through examples. While these recommendations are based on current technology, we anticipate that future advances will push the field further and the molecular ecology community should continue to adopt new approaches that attain the highest quality genome assemblies.

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“…for the first gaze sequence example above) are extracted as features contained in each gaze sequence with look-away fixations (see Appendix A for a detailed example). The use of k-mers to break down the gaze fixation sequences is inspired by k-mer analysis of nucleic acid sequences in bioinformatics [64,65]. Single fixations or sequences of two fixations (2-mers) hold very little information about participants' sequential gaze.…”

Section: Plos Onementioning

confidence: 99%

Seeing through the forest: The gaze path to purchase

et al. 2020

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Eye tracking studies have analyzed the relationship between visual attention to point of purchase marketing elements (price, signage, etc.) and purchase intention. Our study is the first to investigate the relationship between the gaze sequence in which consumers view a display (including gaze aversion away from products) and the influence of consumer (top down) characteristics on product choice. We conducted an in-lab 3 (display size: large, moderate, small) X 2 (price: sale, non-sale) within-subject experiment with 92 persons. After viewing the displays, subjects completed an online survey to provide demographic data, self-reported and actual product knowledge, and past purchase information. We employed a random forest machine learning approach via R software to analyze all possible three-unit subsequences of gaze fixations. Models comparing multiclass F1-macro score and F1micro score of product choice were analyzed. Gaze sequence models that included gaze aversion more accurately predicted product choice in a lab setting for more complex displays. Inclusion of consumer characteristics generally improved model predictive F1-macro and F1-micro scores for less complex displays with fewer plant sizes Consumer attributes that helped improve model prediction performance were product expertise, ethnicity, and previous plant purchases.

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Estimating the k-mer Coverage Frequencies in Genomic Datasets: A Comparative Assessment of the State-of-the-art

Cited by 13 publications

References 41 publications

Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

Complete genomes of the eukaryotic poultry parasite Histomonas meleagridis: linking sequence analysis with virulence / attenuation

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Seeing through the forest: The gaze path to purchase

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