Chromosome-level hybrid <i>de novo</i> genome assemblies as an attainable option for non-model organisms

Jaworski, Coline C.; Allan, Carson W.; Matzkin, Luciano M.

doi:10.1101/748228

Cited by 4 publications

(3 citation statements)

References 37 publications

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“…Despite advances in sequencing technology that have led to dramatic improvements in draft genomes for non‐model species, it remains vital to evaluate the quality and completeness of genome assemblies. As noted above, well known deficiencies in genome assemblies include difficulty in assembling repetitive, duplicated, and GC rich regions that can often be addressed with long‐read sequencing (Sedlazeck et al, 2018), but at the expense of sequencing error which may influence estimates of gene content (Jaworski et al, 2020; Watson & Warr, 2019). The trade‐offs of various sequencing technologies can be offset by applying multiple platforms (Peona et al, 2021; Rhie, McCarthy, et al, 2020), however many chromosome‐level genome assemblies have extensive gaps within and among scaffolds that may hinder utility of these hybrid assemblies for subsequent studies (Domanska et al, 2018; Peona et al, 2021).…”

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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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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“…Although LRs are becoming more widely used for de novo genome assembly, using hybrid approaches (that utilize a complementary SR dataset) is still popular for several reasons: (1) SRs have higher accuracy and can be generated by Illumina sequencers at a high throughput for a lower cost; (2) plenty of SR datasets are already publicly available for many genomes; (3) for some basic tasks such as variant calling (SNV and short indel detection), SRs still provide better resolution owing to their high accuracy, which often motivates researchers to generate SRs even when LRs are in hand; and (4) unlike PacBio assemblies whose accuracy increases with the depth of coverage thanks to their unbiased random error model ( Myers, 2014 ), constructing reference quality genomes solely from ONT reads remains challenging owing to biases in base calling, even with a high coverage ( Koren et al., 2017 ; Antipov et al., 2015 ). As a result, hybrid assembly approaches are still useful ( Jaworski et al., 2019 ; Jiang et al., 2019 ; Kadobianskyi et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

HASLR: Fast Hybrid Assembly of Long Reads

et al. 2020

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Summary Third-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and potentially gap-free assemblies. The larger effective length of their reads has provided a means to overcome the challenges of short to mid-range repeats. Currently, accurate long read assemblers are computationally expensive, whereas faster methods are not as accurate. Moreover, despite recent advances in third-generation sequencing, researchers still tend to generate accurate short reads for many of the analysis tasks. Here, we present HASLR, a hybrid assembler that uses error-prone long reads together with high-quality short reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on most of the samples, while being on par with other assemblers in terms of contiguity and accuracy.

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“…Although LRs are becoming more widely used for de novo genome assembly, using hybrid approaches (that utilize a complementary SR dataset) is still popular for several reasons: (i) SRs have higher accuracy and can be generated by Illumina sequencers at a high throughput for a lower cost; (ii) plenty of SR datasets are already publicly available for many genomes; (iii) for some basic tasks such as variant calling (SNV and short indel detection), SRs still provide better resolution due to their high accuracy which often motivates researchers to generate SRs even when LRs are in hand; and (iv) unlike PacBio assemblies whose accuracy increases with the depth of coverage thanks to their unbiased random error model [23], constructing reference quality genomes solely from ONT reads remains challenging due to biases in base calling, even with a high coverage [14,1]. As a result, hybrid assembly approaches are still useful [8,9,10].…”

Section: Introductionmentioning

confidence: 99%

HASLR: Fast Hybrid Assembly of Long Reads

Haghshenas

Asghari

Stoye

et al. 2020

Preprint

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Third generation sequencing technologies from platforms such as Oxford Nanopore Technologies and Pacific Biosciences have paved the way for building more contiguous assemblies and complete reconstruction of genomes. The larger effective length of the reads generated with these technologies has provided a mean to overcome the challenges of short to mid-range repeats. Currently, accurate long read assemblers are computationally expensive while faster methods are not as accurate. Therefore, there is still an unmet need for tools that are both fast and accurate for reconstructing small and large genomes. Despite the recent advances in third generation sequencing, researchers tend to generate second generation reads for many of the analysis tasks. Here, we present HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.

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Chromosome-level hybrid de novo genome assemblies as an attainable option for non-model organisms

Cited by 4 publications

References 37 publications

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

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

HASLR: Fast Hybrid Assembly of Long Reads

HASLR: Fast Hybrid Assembly of Long Reads

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