scholarly journals Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping v2 (protocols.io.vgse3we)

protocols.io ◽  
2018 ◽  
Author(s):  
Wei Tang ◽  
Xuepeng Sun ◽  
Junyang Yue ◽  
Xiaofeng Tang ◽  
Chen Jiao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Chromatin Interaction ◽  
Single Molecule Sequencing

scholarly journals Efficient long single molecule sequencing for cost effective and accurate sequencing, haplotyping, and de novo assembly

2018 ◽  
Author(s):  
Ou Wang ◽  
Robert Chin ◽  
Xiaofang Cheng ◽  
Michelle Ka Wu ◽  
Qing Mao ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
De Novo ◽  
Low Cost ◽  
Variant Calling ◽  
Cost Effective ◽  
High Quality ◽  
Single Molecule Sequencing ◽  
Single Tube ◽  
Complex Structural

Obtaining accurate sequences from long DNA molecules is very important for genome assembly and other applications. Here we describe single tube long fragment read (stLFR), a technology that enables this a low cost. It is based on adding the same barcode sequence to sub-fragments of the original long DNA molecule (DNA co-barcoding). To achieve this efficiently, stLFR uses the surface of microbeads to create millions of miniaturized barcoding reactions in a single tube. Using a combinatorial process up to 3.6 billion unique barcode sequences were generated on beads, enabling practically non-redundant co-barcoding with 50 million barcodes per sample. Using stLFR, we demonstrate efficient unique co-barcoding of over 8 million 20-300 kb genomic DNA fragments. Analysis of the genome of the human genome NA12878 with stLFR demonstrated high quality variant calling and phasing into contigs up to N50 34 Mb. We also demonstrate detection of complex structural variants and complete diploid de novo assembly of NA12878. These analyses were all performed using single stLFR libraries and their construction did not significantly add to the time or cost of whole genome sequencing (WGS) library preparation. stLFR represents an easily automatable solution that enables high quality sequencing, phasing, SV detection, scaffolding, cost-effective diploid de novo genome assembly, and other long DNA sequencing applications.

scholarly journals A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Xuchen Yang ◽  
Minghui Kang ◽  
Yanting Yang ◽  
Haifeng Xiong ◽  
Mingcheng Wang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
De Novo ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Single Molecule Sequencing ◽  
Data Matching ◽  
Long Reads ◽  
Autumn Leaf ◽  
Chromosome Level

AbstractThe deciduous Chinese tupelo (Nyssa sinensis Oliv.) is a popular ornamental tree for the spectacular autumn leaf color. Here, using single-molecule sequencing and chromosome conformation capture data, we report a high-quality, chromosome-level genome assembly of N. sinensis. PacBio long reads were de novo assembled into 647 polished contigs with a total length of 1,001.42 megabases (Mb) and an N50 size of 3.62 Mb, which is in line with genome sizes estimated using flow cytometry and the k-mer analysis. These contigs were further clustered and ordered into 22 pseudo-chromosomes based on Hi-C data, matching the chromosome counts in Nyssa obtained from previous cytological studies. In addition, a total of 664.91 Mb of repetitive elements were identified and a total of 37,884 protein-coding genes were predicted in the genome of N. sinensis. All data were deposited in publicly available repositories, and should be a valuable resource for genomics, evolution, and conservation biology.

scholarly journals Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 788 ◽  
Author(s):  
Luke J Tallon ◽  
Xinyue Liu ◽  
Sasisekhar Bennuru ◽  
Marcus C Chibucos ◽  
Alvaro Godinez ◽  
...  
Keyword(s):  
Single Molecule ◽  
Causative Agent ◽  
Genome Assembly ◽  
Clinical Specimen ◽  
Loa Loa ◽  
Single Molecule Sequencing

scholarly journals Cryptocurrencies and Zero Mode Wave guides: An unclouded path to a more contiguous Cannabis sativa L. genome assembly.

2018 ◽  
Author(s):  
Kevin McKernan ◽  
Yvonne Helbert ◽  
Liam T. Kane ◽  
Heather Ebling ◽  
Lei Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Cannabis Sativa ◽  
Zero Mode ◽  
Gene Clusters ◽  
Type Ii ◽  
Single Molecule Sequencing ◽  
Combined Use ◽  
Wave Guides ◽  
Repeat Expansions

We describe the use of a Decentralized Autonomous Organization (DAO) to crypto-fund the single molecule sequencing and publication of a Type II Cannabis plant. This resulted in the construction of the most contiguous Cannabis genome assembly to date. The combined use of the Dash cryptocurrency, DAOs, and Pacific Biosciences sequencing delivered a 1.03 Gb genome with a N50 of 665Kb in 77 days from funding to public upload. This represents a 230 fold improvement in the contiguity of the first cannabis assemblies in 2011 and a 4 fold improvement over all cannabis assemblies to date. 34Gb of additional sequencing pushed the assembly to a N50 of 3.8Mb. Hi-C data from Phase Genomics further scaffolded the assembly to 35 contigs at an N50 of 74Mb but requires additional curation. The genome is partially phased and larger than previously reported (2N = 1.33Gb). The CBCA, THCA and CBDA synthase gene clusters have been phased onto respective contigs demonstrating tandem repeat expansions.

scholarly journals SMARTdenovo: a de novo assembler using long noisy reads

Gigabyte ◽  
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.

scholarly journals Single-Molecule Sequencing Assists Genome Assembly Improvement and Structural Variation Inference

2016 ◽  
Vol 9 (7) ◽  
pp. 1085-1087
Author(s):  
Jun Yan ◽  
Shuwei Lv ◽  
Min Hu ◽  
Zhaoxu Gao ◽  
Hang He ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Structural Variation ◽  
Single Molecule Sequencing

scholarly journals SMARTdenovo: A de novo Assembler Using Long Noisy Reads

2020 ◽  
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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