Fast and accurate assembly of Nanopore reads via progressive error correction and adaptive read selection

AbstractAlthough long Nanopore reads are advantageous in de novo genome assembly, applying Nanopore reads in genomic studies is still hindered by their complex errors. Here, we developed NECAT, an error correction and de novo assembly tool designed to overcome complex errors in Nanopore reads. We proposed an adaptive read selection and two-step progressive method to quickly correct Nanopore reads to high accuracy. We introduced a two-stage assembler to utilize the full length of Nanopore reads. NECAT achieves superior performance in both error correction and de novo assembly of Nanopore reads. NECAT requires only 7,225 CPU hours to assemble a 35X coverage human genome and achieves a 2.28-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line showed an NG50 of 29 Mbp. The high-quality assembly of Nanopore reads can significantly reduce false positives in structure variation detection.

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Efficient assembly of nanopore reads via highly accurate and intact error correction

Nature Communications ◽

10.1038/s41467-020-20236-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ying Chen ◽

Fan Nie ◽

Shang-Qian Xie ◽

Ying-Feng Zheng ◽

Qi Dai ◽

...

Keyword(s):

Error Correction ◽

Error Rate ◽

De Novo ◽

Superior Performance ◽

High Error Rate ◽

De Novo Genome Assembly ◽

Structure Variation ◽

Final Assembly ◽

De Novo Assembling ◽

Assembly Tool

AbstractLong nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.

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SMARTdenovo: a de novo assembler using long noisy reads

Gigabyte ◽

10.46471/gigabyte.15 ◽

2021 ◽

Vol 2021 ◽

pp. 1-9

Author(s):

Hailin Liu ◽

Shigang Wu ◽

Alun Li ◽

Jue Ruan

Keyword(s):

Error Correction ◽

Single Molecule ◽

Genome Assembly ◽

De Novo ◽

Structural Variants ◽

High Quality ◽

Single Molecule Sequencing ◽

Long Read ◽

Reference Quality

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It has also been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler SMARTdenovo, a single-molecule sequencing (SMS) assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a rapid assembler, which, unlike contemporaneous SMS assemblers, does not require highly accurate raw reads for error correction. It has performed well in the evaluation of congeneric assemblers and has been successfully users for various assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015; here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

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SMARTdenovo: A de novo Assembler Using Long Noisy Reads

10.20944/preprints202009.0207.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Hailin Liu ◽

Shigang Wu ◽

Alun Li ◽

Jue Ruan

Keyword(s):

Error Correction ◽

Single Molecule ◽

Genome Assembly ◽

De Novo ◽

Structural Variants ◽

High Quality ◽

De Novo Genome Assembly ◽

Single Molecule Sequencing ◽

Long Read ◽

Reference Quality

Long-read single-molecule sequencing has revolutionized de novo genome assembly and enabled the automated reconstruction of reference-quality genomes. It also has been widely used to study structural variants, phase haplotypes and more. Here, we introduce the assembler— SMARTdenovo, which is an SMS assembler that follows the overlap-layout-consensus (OLC) paradigm. SMARTdenovo (RRID: SCR_017622) was designed to be a fast assembler that did not require highly accurate raw reads for error correction, unlike other, contemporaneous SMS assemblers. It has performed well for evaluating congeneric assemblers and has been successful for a variety of assembly projects. It is compatible with Canu for assembling high-quality genomes, and several of the assembly strategies in this program have been incorporated into subsequent popular assemblers. The assembler has been in use since 2015, and here we provide information on the development of SMARTdenovo and how to implement its algorithms into current projects.

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise

10.1101/2019.12.19.882399 ◽

2019 ◽

Cited By ~ 5

Author(s):

Valentina Peona ◽

Mozes P.K. Blom ◽

Luohao Xu ◽

Reto Burri ◽

Shawn Sullivan ◽

...

Keyword(s):

Dark Matter ◽

Genome Assembly ◽

Sex Chromosome ◽

De Novo ◽

Model Organism ◽

Technology Choice ◽

High Quality ◽

Sequencing Technologies ◽

Downstream Analysis ◽

Genome Assemblies

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.

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Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

10.1101/2021.11.23.469778 ◽

2021 ◽

Author(s):

Xinxin Yi ◽

Jing Liu ◽

Shengcai Chen ◽

Hao Wu ◽

Min Liu ◽

...

Keyword(s):

Nitrogen Fixation ◽

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Genomic Analysis ◽

Comparative Genomic ◽

High Quality ◽

Genome Wide ◽

A Genome ◽

Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

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De Novo Assembly of a High-Quality Reference Genome for the Horned Lark (Eremophila alpestris)

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400846 ◽

2019 ◽

Vol 10 (2) ◽

pp. 475-478 ◽

Cited By ~ 3

Author(s):

Nicholas A. Mason ◽

Paulo Pulgarin ◽

Carlos Daniel Cadena ◽

Irby J. Lovette

Keyword(s):

Genome Assembly ◽

De Novo ◽

Single Copy ◽

Single Copy Gene ◽

High Quality ◽

Data Set ◽

Copy Gene ◽

Assembly Pipeline ◽

Horned Lark ◽

Gene Orthologs

The Horned Lark (Eremophila alpestris) is a small songbird that exhibits remarkable geographic variation in appearance and habitat across an expansive distribution. While E. alpestris has been the focus of many ecological and evolutionary studies, we still lack a highly contiguous genome assembly for the Horned Lark and related taxa (Alaudidae). Here, we present CLO_EAlp_1.0, a highly contiguous assembly for E. alpestris generated from a blood sample of a wild, male bird captured in the Altiplano Cundiboyacense of Colombia. By combining short-insert and mate-pair libraries with the ALLPATHS-LG genome assembly pipeline, we generated a 1.04 Gb assembly comprised of 2713 scaffolds, with a largest scaffold size of 31.81 Mb, a scaffold N50 of 9.42 Mb, and a scaffold L50 of 30. These scaffolds were assembled from 23685 contigs, with a largest contig size of 1.69 Mb, a contig N50 of 193.81 kb, and a contig L50 of 1429. Our assembly pipeline also produced a single mitochondrial DNA contig of 14.00 kb. After polishing the genome, we identified 94.5% of single-copy gene orthologs from an Aves data set and 97.7% of single-copy gene orthologs from a vertebrata data set, which further demonstrates the high quality of our assembly. We anticipate that this genomic resource will be useful to the broader ornithological community and those interested in studying the evolutionary history and ecological interactions of larks, which comprise a widespread, yet understudied lineage of songbirds.

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A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae

Genome Biology and Evolution ◽

10.1093/gbe/evz269 ◽

2019 ◽

Vol 12 (1) ◽

pp. 3635-3646 ◽

Cited By ~ 3

Author(s):

Arnab Ghosh ◽

Matthew G Johnson ◽

Austin B Osmanski ◽

Swarnali Louha ◽

Natalia J Bayona-Vásquez ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Genome Structure ◽

Protein Domain ◽

Alligator Mississippiensis ◽

Structure Evolution ◽

Functional Protein ◽

High Quality ◽

Saltwater Crocodile ◽

Crocodylus Porosus

Abstract Crocodilians are an economically, culturally, and biologically important group. To improve researchers’ ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple noncoding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, 10 in C. porosus and 6 in Alligator mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological, and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.

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High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-19-0280-a ◽

2020 ◽

Vol 33 (5) ◽

pp. 718-720

Author(s):

Karthi Natesan ◽

Ji Yeon Park ◽

Cheol-Woo Kim ◽

Dong Suk Park ◽

Young-Seok Kwon ◽

...

Keyword(s):

Downy Mildew ◽

De Novo ◽

Gc Content ◽

Comparative Genomic ◽

High Quality ◽

Sequencing Platform ◽

Peronospora Destructor ◽

Genomic Studies ◽

Genome Assemblies ◽

High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

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A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II system

GigaScience ◽

10.1093/gigascience/giz122 ◽

2019 ◽

Vol 8 (10) ◽

Cited By ~ 12

Author(s):

Sarah B Kingan ◽

Julie Urban ◽

Christine C Lambert ◽

Primo Baybayan ◽

Anna K Childers ◽

...

Keyword(s):

Invasive Species ◽

Genome Assembly ◽

De Novo ◽

Fragment Size ◽

High Quality ◽

De Novo Genome Assembly ◽

Lycorma Delicatula ◽

Long Read ◽

Genome Assemblies ◽

High Quality Genome

ABSTRACT Background A high-quality reference genome is an essential tool for applied and basic research on arthropods. Long-read sequencing technologies may be used to generate more complete and contiguous genome assemblies than alternate technologies; however, long-read methods have historically had greater input DNA requirements and higher costs than next-generation sequencing, which are barriers to their use on many samples. Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell. The spotted lanternfly is an invasive species recently discovered in the northeastern United States that threatens to damage economically important crop plants in the region. Results The DNA from 1 individual was used to make 1 standard, size-selected library with an average DNA fragment size of ∼20 kb. The library was run on 1 Sequel II SMRT Cell 8M, generating a total of 132 Gb of long-read sequences, of which 82 Gb were from unique library molecules, representing ∼36× coverage of the genome. The assembly had high contiguity (contig N50 length = 1.5 Mb), completeness, and sequence level accuracy as estimated by conserved gene set analysis (96.8% of conserved genes both complete and without frame shift errors). Furthermore, it was possible to segregate more than half of the diploid genome into the 2 separate haplotypes. The assembly also recovered 2 microbial symbiont genomes known to be associated with L. delicatula, each microbial genome being assembled into a single contig. Conclusions We demonstrate that field-collected arthropods can be used for the rapid generation of high-quality genome assemblies, an attractive approach for projects on emerging invasive species, disease vectors, or conservation efforts of endangered species.

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A high-quality de novo genome assembly from a single parasitoid wasp

10.1101/2020.07.13.200725 ◽

2020 ◽

Cited By ~ 1

Author(s):

Xinhai Ye ◽

Yi Yang ◽

Zhaoyang Tian ◽

Le Xu ◽

Kaili Yu ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Parasitoid Wasp ◽

Genome Comparison ◽

Single Individual ◽

High Quality ◽

De Novo Genome Assembly ◽

Low Input ◽

A Genome ◽

High Level

AbstractSequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines. Although few studies sequenced a single small insect with about 100 ng DNA as input, it may still be challenging for many small organisms to obtain such amount of DNA from a single individual. Here, we use 20 ng DNA as input, and present a high-quality genome assembly for a single haploid male parasitoid wasp (Habrobracon hebetor) using Nanopore and Illumina. Because of the low input DNA, a whole genome amplification (WGA) method is used before sequencing. The assembled genome size is 131.6 Mb with a contig N50 of 1.63 Mb. A total of 99% Benchmarking Universal Single-Copy Orthologs are detected, suggesting the high level of completeness of the genome assembly. Genome comparison between H. hebetor and its relative Bracon brevicornis shows a high-level genome synteny, indicating the genome of H. hebetor is highly accurate and contiguous. Our study provides an example for de novo assembling a genome from ultra-low input DNA, and will be used for sequencing projects of small sized species and rare samples, haploid genomics as well as population genetics of small sized species.

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