KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

Mapleson, Daniel; Accinelli, Gonzalo Garcia; Kettleborough, George; Wright, Jonathan; Clavijo, Bernardo

doi:10.1093/bioinformatics/btw663

Cited by 434 publications

(337 citation statements)

References 10 publications

Supporting

Mentioning

311

Contrasting

Order By: Relevance

“…The assemblies were checked for contamination and further manually assessed and corrected using gEVAL [25]. The Kmer Analysis Toolkit (KAT) version 2.4.2 [26] was used to compare k-mers from the 10X Illumina data to k-mers in each of the haplotype-resolved assemblies, and in the combined diploid assembly representing both haplotypes. Phasing of the assembled contigs and scaffolds was visualised using the parental k-mer databases produced by Canu [27].…”

Section: Trio Binning Genome Assemblymentioning

confidence: 99%

A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

Yen

McCarthy

Galarza

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Diploid genome assembly is typically impeded by heterozygosity, as it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution which exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. Findings: We produced a highquality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ~1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked-reads. Both assemblies are highly contiguous (mean scaffold N50: 8.2Mb) and complete (mean BUSCO completeness: 97.3%), with complete annotations and 31 chromosomes identified through karyotyping. We employed the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from five populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. Conclusions:We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling highly heterozygous genomes. Using this assembly, we provide genomic insights into geographic population structure of Arctia plantaginis.

show abstract

Section: Trio Binning Genome Assemblymentioning

confidence: 99%

A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

Yen

McCarthy

Galarza

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The raw data from both experiments were examined using fastQC v.0.11.8 60 and K-mer analysis v.2.4.1 (KAT; 61 . Long-reads data were also examined using SMRT link analysis v.6.0.0.47836 and stsPlots.…”

Section: Genome Quality Controlmentioning

confidence: 99%

The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions

Souza¹,

Amaral²,

Batista³

et al. 2020

Preprint

View full text Add to dashboard Cite

Corals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some species like Tubastraea coccinea and T. tagusensis have been spreading very fast replacing the native ones which affect the local environment and decrease biodiversity of corals and other organisms associated with them. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for both conservation and management of invasive species. In this circumstance, it is expected that genome sequencing would provide powerful insights that could lead to better strategies for prevention, management, and control of this and other invasive species. Here, we present three genomes of Tubastraea spp. in one of the most comprehensive biological studies of corals, that includes flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The genome of T. tagusensis is organized in 23 chromosomes pairs and has 1.1 Gb, the T. coccinea genome is organized in 22 chromosome pairs and has 806 Mb, and the Tubastraea sp. genome is organized in 21 chromosome pairs and has 795 Mb. The hybrid assembly of T. tagusensis using short and long-reads has a N50 of 227,978 bp, 7,996 contigs and high completeness estimated as 91.6% of BUSCO complete genes, of T. coccinea has a N50 of 66,396 bp, 17,214 contigs and 88.1% of completeness , and of Tubastraea sp. has a N50 of 82,672 bp, 12,922 contigs and also 88.1% of completeness . We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. We provide evidence for exclusive Scleractinia and Tubastraea gene content related to adhesion and immunity. The Tubastraea spp. genomes are a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral genus, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of coral species, whether invasive or threatened.

show abstract

“…Secondly, we obtained the unmapped sequencing reads against our genome assembly and re-assembled them into ~359 Mb sequences which contained ~95.05% repetitive sequences ( Supplementary Table 5 ). Using KAT sect tool[26], we also calculated the sequencing depth distribution of flanking sequences of gap regions, we observed that ~71% of sequences nearby junction regions have higher sequencing depth ( Supplementary Fig. 3 ), indicating that majority of the gap regions were repetitive sequences.…”

Section: Analysesmentioning

confidence: 99%

Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

Fan¹,

Fu²,

Yang

et al. 2018

Preprint

View full text Add to dashboard Cite

Panax notoginseng is a traditional Chinese herb with high medicinal and economic value. There has been considerable research on the pharmacological activities of ginsenosides contained in Panax spp.; however, very little is known about the ginsenoside biosynthetic pathway. We reported the first de novo genome of 2.36 Gb of sequences from P. notoginseng with 35,451 protein-encoding genes. Compared to other plants, we found notable gene family contraction of disease-resistance genes in P. notoginseng, but notable expansion for several ATP-binding cassette (ABC) All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The 4, 2018; transporter subfamilies, such as the Gpdr subfamily, indicating that ABCs might be an additional mechanism for the plant to cope with biotic stress. Combining eight transcriptomes of roots and aerial parts, we identified several key genes, their transcription factor binding sites and all their family members involved in the synthesis pathway of ginsenosides in P. notoginseng, including dammarenediol synthase, CYP716 and UGT71. The complete genome analysis of P. notoginseng, the first in genus Panax, will serve as an important reference sequence for improving breeding and cultivation of this important nutraceutical and medicinal but vulnerable plant species.copyright holder for this preprint (which . http://dx.doi.org/10.1101/362046 doi: bioRxiv preprint first posted online Jul.All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

show abstract

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies

Cited by 434 publications

References 10 publications

A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

The genomes of invasive coral Tubastraea spp. (Dendrophylliidae) as tool for the development of biotechnological solutions

Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

Contact Info

Product

Resources

About