Assemblytics: a web analytics tool for the detection of variants from an assembly

Nattestad, Maria; Schatz, Michael C.

doi:10.1093/bioinformatics/btw369

Cited by 322 publications

(353 citation statements)

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“…SNPs and small indels were then identified if they were supported by at least four mapped reads. To detect large SVs (≥50 bp), genome sequences of ‘97103’ and ‘Charleston Gray’ were aligned using Minimap2 (Li, ), and based on the alignment indels and tandem/repeat expansions/contractions were identified using Assemblytics (Nattestad and Schatz, ). To confirm the identified SVs, reads generated from one genome were aligned to the opposite genome using bowtie (Langmead et al ., ) allowing one mismatch.…”

Section: Methodsmentioning

confidence: 99%

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Wang

Reddy

et al. 2019

Plant Biotechnology Journal

103

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Summary Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high‐quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping‐by‐sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high‐quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome‐wide association studies. The high‐quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.

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Section: Methodsmentioning

confidence: 99%

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Wang

Reddy

et al. 2019

Plant Biotechnology Journal

103

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“…For instance, Assemblytics (Nattestad and Schatz, 2016) . In plants, population analysis of 302 soybean re-sequencing lines showed that many CNVs could be targets of artificial selection in addition to the SNPs.…”

Section: Algorithmic Advancement To Detect Structural Variationsmentioning

confidence: 99%

Cataloging Plant Genome Structural Variations

Zhang¹,

Liang²,

Tang³

2018

Current Issues in Molecular Biology

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Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next-generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the 'hidden' diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs. Specific examples are chosen to demonstrate the genetic basis for phenotype diversity in model plant and major agricultural crops. Additionally, development of new genomic mapping technologies, including optical mapping and long read sequencing, as well as improved computational algorithms associated with these technologies have helped to pinpoint the exact nature and location of genomic SVs with much better resolution and precision. Future direction of plant research on SVs should focus on the population level to build a comprehensive catalogue of SVs, leading to full assessment of their impact on biological diversity.

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“…We analyzed the resulting alignment using Assemblytics [12], with results available at: http://assemblytics.com/analysis.php?code= human. We also downloaded the MHAP CHM1 assembly (accession: GCA 000772585)…”

Section: Supplementary Note 3 Obtaining Chm1-specific Sequencesmentioning

confidence: 99%

“…We analyzed the resulting alignment using Assemblytics [12], with the results available at: http://assemblytics.com/ analysis.php?code=sIOvqHUKNaCpU8NXdcTS. This assembly is like the one used above (accession: GCA 000772585), but with low-support contigs (having fewer than 50 supporting reads) removed.…”

Section: Supplementary Note 3 Obtaining Chm1-specific Sequencesmentioning

confidence: 99%

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A tandem simulation framework for predicting mapping quality

Langmead

2017

Preprint

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Read alignment is the first step in most sequencing data analyses. Because a read's point of origin can be ambiguous, aligners report a mapping quality: the probability the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. We describe a framework for predicting mapping qualities that works by simulating a set of tandem reads, similar to the input reads in important ways, but for which the true point of origin is known. We implement this in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.

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Assemblytics: a web analytics tool for the detection of variants from an assembly

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 322 publications

References 6 publications

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Cataloging Plant Genome Structural Variations

A tandem simulation framework for predicting mapping quality

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