ARCS: scaffolding genome drafts with linked reads

Yeo, Sarah; Coombe, Lauren; Rm, Warren; Chu, Justin; Birol, İnanç

doi:10.1093/bioinformatics/btx675

Cited by 176 publications

(186 citation statements)

References 20 publications

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“…Finally, we iteratively scaffolded the de-duplicated Flye assembly using our 10X Genomics linked-read data. We ran two iterations of Scaff10x v4.0 (https://github.com/wtsi-hpag/Scaff10X) with the parameters "-longread 1 -edge 45000block 45000" followed by Tigmint v1.1.2 (Jackman et al 2018) with default settings, which identifies misassemblies, breaks the assembly and performs a final round of scaffolding with ARCS (Yeo et al 2018).…”

Section: Sequencing and De Novo Assembly Of A Pisum Clone Jic1mentioning

confidence: 99%

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Mathers

Wouters

Mugford

et al. 2020

Preprint

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Large-scale chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera (flies and mosquitoes) and Lepidoptera (butterflies and moths) have high levels of chromosome conservation. Whether this truly reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids -an important group of hemipteran plant pests -using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published chromosome-scale assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganisation over the last 30 million years, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (M. persicae and A. pisum) and Aphidini (R. maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies to chromosome-level assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny and we detect only two chromosome fusion or fission events. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.

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Section: Sequencing and De Novo Assembly Of A Pisum Clone Jic1mentioning

confidence: 99%

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Mathers

Wouters

Mugford

et al. 2020

Preprint

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“…DNA prepared from pooled worms was used to generate 10X sequencing libraries, which were subsequently sequenced on a HiSeq 2500 using 250 bp PE reads. Reads were mapped using bwa mem (v0.7.17-r1188), followed by scaffolding using ARCS [75] and LINKS [76] . A single scaffold was generated using this approach, merging the two major X-linked scaffolds as well as two short sequences putatively identified as being X-linked but previously unplaced ( Additional file 1: Figure S2 ).…”

Section: Iterative Improvement Of the Genome Assemblymentioning

confidence: 99%

Extensive genomic and transcriptomic variation defines the chromosome-scale assembly ofHaemonchus contortus, a model gastrointestinal worm

Doyle

Tracey

Laing

et al. 2020

Preprint

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Background Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants, and has become the key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Two draft genome assemblies for H. contortus were reported in 2013, however, both were highly fragmented, incomplete, and differed from one another in important respects. While the introduction of long-read sequencing has significantly increased the rate of production and contiguity of de novo genome assemblies broadly, achieving high quality genome assemblies for small, genetically diverse, outcrossing eukaryotic organisms such as H. contortus remains a significant challenge. ResultsHere, we report using PacBio long read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome. We show a remarkable pattern of almost complete conservation of chromosome content (synteny) with Caenorhabditis elegans , but almost no conservation of gene order. Long-read transcriptome sequence data has allowed us to define coordinated transcriptional regulation throughout the life cycle of the parasite, and refine our understanding of cisand trans -splicing relative to that observed in C. elegans .Finally, we use this assembly to give a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. ConclusionsThe H. contortus MHco3(ISE).N1 genome assembly presented here represents the most contiguous and resolved nematode assembly outside of the Caenorhabditis genus to date, together with one of the highest-quality set of predicted gene features. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes, and extends the experimental tractability of this model parasitic nematode in understanding pathogen biology, drug discovery and vaccine development, and important adaptive traits such as drug resistance.

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“…Chromosome conformation capture [4] provides pairs of reads that have a high probability to originate from the same chromosome and Chromium 10X [5] uses a droplet mechanism to ensure that a pack of reads come from a single DNA fragment of up to hundreds of thousands base pairs. Both of these techniques have been shown to produce assembly continuity comparable to TGS assembly [6,7,8]. SGS reads are also used jointly with long reads to compensate the latter's high error rate (and systematic homopolymer errors in the case of ONT reads [9]) in a costefficient way [10].…”

Section: On the Use Of Short Reads As Long Reads Are Risingmentioning

confidence: 99%

Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs

Limasset

Flot

Peterlongo³

2019

Preprint

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Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or consider reads as mere suites of k-mers, without taking into account their full-length read information. Results We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond. Availability and ImplementationThe implementation is open source and available at http: //github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package.

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ARCS: scaffolding genome drafts with linked reads

Cited by 176 publications

References 20 publications

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Extensive genomic and transcriptomic variation defines the chromosome-scale assembly ofHaemonchus contortus, a model gastrointestinal worm

Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs

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