A Sequence Distance Graph framework for genome assembly and analysis

Yanes, Luis; Accinelli, Gonzalo Garcia; Wright, Jonathan; Ward, Ben J.; Clavijo, Bernardo

doi:10.12688/f1000research.20233.1

Cited by 4 publications

(3 citation statements)

References 17 publications

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“…A canonical collapsed De Bruijn Graph (DBG) is first constructed in Sequence Distance Graph Threader (SDG-Threader)(14) from the short reads, which is then cleaned and simplified. Further repeat resolution is completed by finding unique paths between nodes representing haploid content, followed by canonical repeat resolution using long reads.…”

Section: Methodsmentioning

confidence: 99%

Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome

Hodgkinson

Wright

Accinelli

et al. 2022

Preprint

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Fragilariopsis cylindrus CCMP1102 is characterised by a complex genome with significant levels of heterozygosity between haplotypes, > 35% repeats, and an unknown karyotype. This complexity hindered prior assemblies, which show coverage discrepancies indicative of incompleteness. Here, we use a k-mer spectra analysis to reveal the coverage signature for a third haplotype. We applied a novel haplotype-specific assembly method to reconstruct the F. cylindrus CCMP1102 genome, producing 10 fully assembled chromosomes capped by telomeres, and a putative chromosome with a single breakpoint. Our analysis shows triploidy, two cases of aneuploidy, and several truncations. We also present evidence that F. cylindrus reproduces sexually. Taken together, our analytical approach is capable of haplotype-resolved assemblies from structurally complex, polyploid genomes, making it suitable for complex genomes of non-model organisms, including those with unknown karyotype.

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Section: Methodsmentioning

confidence: 99%

Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome

Hodgkinson

Wright

Accinelli

et al. 2022

Preprint

Self Cite

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“…This has resulted in the development of the FASTG format ( http://fastg.sourceforge.net , accessed 25 May 2021) and, more recently and with wider adoption, the graphical fragment assembly (GFA) format for assembly graph files ( https://github.com/GFA-spec/GFA-spec , accessed 25 May 2021). These have been implemented in a number of tools including recent versions of ABySS ( Jackman, 2017 ), SPAdes ( Bankevich, 2012 ), metaSPAdes and SDG ( Yanes, 2019 ). Other tools have addressed the problem of analysing the quantity of sequencing data that is currently available, particularly in metagenomics.…”

Section: Introductionmentioning

confidence: 99%

Capturing variation in metagenomic assembly graphs with MetaCortex

et al. 2023

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Motivation The assembly of contiguous sequence from metagenomic samples presents a particular challenge, due to the presence of multiple species, often closely related, at varying levels of abundance. Capturing diversity within species, for example viral haplotypes, or bacterial strain-level diversity, is even more challenging. Results We present MetaCortex, a metagenome assembler that captures intra-species diversity by searching for signatures of local variation along assembled sequences in the underlying assembly graph and outputting these sequences in sequence graph format. We show that MetaCortex produces accurate assemblies with higher genome coverage and contiguity than other popular metagenomic assemblers on mock viral communities with high levels of strain level diversity, and on simulated communities containing simulated strains. Availability Source code is freely available to download from https://github.com/SR-Martin/metacortex, is implemented in C and supported on MacOS and Linux. The version used for the results presented in this paper is available at doi.org/10.5281/zenodo.7273627. Supplementary information Supplementary data are available at Bioinformatics online.

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“…This has resulted in the development of the FASTG format [12] and, more recently and with wider adoption, the graphical fragment assembly (GFA) format for assembly graph files [13]. These have been implemented in a number of tools including recent versions of ABySS [14], SPAdes [15] and SDG [16]. However, as yet, specialist metagenomic assembly tools lack the ability to capture variation through GFA output.…”

Section: Introductionmentioning

confidence: 99%

Capturing variation in metagenomic assembly graphs with MetaCortex

Martin

Ayling

Patrono

et al. 2021

Preprint

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The assembly of contiguous sequence from metagenomic samples presents a particular challenge, due to the presence of multiple species, often closely related, at varying levels of abundance. Capturing diversity within species, for example viral haplotypes, or bacterial strain-level diversity, is even more challenging. We present MetaCortex, a metagenome assembler based on data structures from the Cortex de novo assembler. MetaCortex captures intra-species diversity by searching for signatures of local variation along assembled sequences in the underlying assembly graph and outputting these sequences in sequence graph format. MetaCortex also implements a novel assembly algorithm for representing intra-species diversity in standard linear format. We show that MetaCortex produces accurate assemblies with higher genome coverage and contiguity than other popular metagenomic assemblers on mock viral communities with high levels of strain level diversity, and on simulated communities containing simulated strains. We also show that accuracy can be increased further by using the sequence graph produced by MetaCortex to create highly accurate single contig sequences.

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A Sequence Distance Graph framework for genome assembly and analysis

Cited by 4 publications

References 17 publications

Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome

Disentangling the genomic complexity of the Fragilariopsis cylindrus (CCMP1102) genome

Capturing variation in metagenomic assembly graphs with MetaCortex

Capturing variation in metagenomic assembly graphs with MetaCortex

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