scholarly journals A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 332 ◽  
Author(s):  
Krishnamoorthy Srikanth ◽  
Jong-Eun Park ◽  
Dajeong Lim ◽  
Jihye Cha ◽  
Sang-Rae Cho ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Sequence Data ◽  
Whole Genome ◽  
Library Preparation ◽  
Preparation Methods ◽  
Short Read ◽  
Long Read ◽  
Hanwoo Cattle ◽  
Genome Scale ◽  
Sample Preparation Methods

Until recently, genome-scale phasing was limited due to the short read sizes of sequence data. Though the use of long-read sequencing can overcome this limitation, they require extensive error correction. The emergence of technologies such as 10X genomics linked read sequencing and Hi-C which uses short-read sequencers along with library preparation protocols that facilitates long-read assemblies have greatly reduced the complexities of genome scale phasing. Moreover, it is possible to accurately assemble phased genome of individual samples using these methods. Therefore, in this study, we compared three phasing strategies which included two sample preparation methods along with the Long Ranger pipeline of 10X genomics and HapCut2 software, namely 10X-LG, 10X-HapCut2, and HiC-HapCut2 and assessed their performance and accuracy. We found that the 10X-LG had the best phasing performance amongst the method analyzed. They had the highest phasing rate (89.6%), longest adjusted N50 (1.24 Mb), and lowest switch error rate (0.07%). Moreover, the phasing accuracy and yield of the 10X-LG stayed over 90% for distances up to 4 Mb and 550 Kb respectively, which were considerably higher than 10X-HapCut2 and Hi-C Hapcut2. The results of this study will serve as a good reference for future benchmarking studies and also for reference-based imputation in Hanwoo.

scholarly journals Paragraph: a graph-based structural variant genotyper for short-read sequence data

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sai Chen ◽  
Peter Krusche ◽  
Egor Dolzhenko ◽  
Rachel M. Sherman ◽  
Roman Petrovski ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Structural Variations ◽  
Short Read ◽  
Three Samples ◽  
Genomics Research ◽  
Long Read ◽  
Short Read Sequence ◽  
Population Scale

AbstractAccurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long-read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples of diverse ancestry. Our analysis shows that Paragraph has better accuracy than other existing genotypers and can be applied to population-scale studies.

scholarly journals De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 618 ◽  
Author(s):  
Michael Liem ◽  
Hans J. Jansen ◽  
Ron P. Dirks ◽  
Christiaan V. Henkel ◽  
G. Paul H. van Heusden ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
New Technology ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Short Read ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Before And After ◽  
Long Read

Background: The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for de novo assembly of complex genomes without using other technologies. Furthermore, Nanopore data combined with other sequencing technologies is highly useful for accurate annotation of all genes in the genome. In this manuscript we used nanopore sequencing as a tool to classify yeast strains. Methods: We compared various technical and software developments for the nanopore sequencing protocol, showing that the R9 chemistry is, as predicted, higher in quality than R7.3 chemistry. The R9 chemistry is an essential improvement for assembly of the extremely AT-rich mitochondrial genome. We double corrected assemblies from four different assemblers with PILON and assessed sequence correctness before and after PILON correction with a set of 290 Fungi genes using BUSCO. Results: In this study, we used this new technology to sequence and de novo assemble the genome of a recently isolated ethanologenic yeast strain, and compared the results with those obtained by classical Illumina short read sequencing. This strain was originally named Candida vartiovaarae (Torulopsis vartiovaarae) based on ribosomal RNA sequencing. We show that the assembly using nanopore data is much more contiguous than the assembly using short read data. We also compared various technical and software developments for the nanopore sequencing protocol, showing that nanopore-derived assemblies provide the highest contiguity. Conclusions: The mitochondrial and chromosomal genome sequences showed that our strain is clearly distinct from other yeast taxons and most closely related to published Cyberlindnera species. In conclusion, MinION-mediated long read sequencing can be used for high quality de novo assembly of new eukaryotic microbial genomes.

scholarly journals De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 618 ◽  
Author(s):  
Hans J. Jansen ◽  
Ron P. Dirks ◽  
Michael Liem ◽  
Christiaan V. Henkel ◽  
G. Paul H. van Heusden ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
New Technology ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Short Read ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Wild Type Yeast

Background: The introduction of the MinIONTM sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. It has been shown that the nanopore sequence data, in combination with other sequencing technologies, is highly useful for accurate annotation of all genes in the genome. However, it also offers great potential for de novo assembly of complex genomes without using other technologies. In this manuscript we used nanopore sequencing as a tool to classify yeast strains. Methods: We compared various technical and software developments for the nanopore sequencing protocol, showing that the R9 chemistry is, as predicted, higher in quality than R7.3 chemistry. The R9 chemistry is an essential improvement for assembly of the extremely AT-rich mitochondrial genome. Results: In this study, we used this new technology to sequence and de novo assemble the genome of a recently isolated ethanologenic yeast strain, and compared the results with those obtained by classical Illumina short read sequencing. This strain was originally named Candida vartiovaarae (Torulopsis vartiovaarae) based on ribosomal RNA sequencing. We show that the assembly using nanopore data is much more contiguous than the assembly using short read data. Conclusions: The mitochondrial and chromosomal genome sequences showed that our strain is clearly distinct from other yeast taxons and most closely related to published Cyberlindnera species. In conclusion, MinION-mediated long read sequencing can be used for high quality de novo assembly of new eukaryotic microbial genomes.

scholarly journals Paragraph: A graph-based structural variant genotyper for short-read sequence data

2019 ◽  
Author(s):  
Sai Chen ◽  
Peter Krusche ◽  
Egor Dolzhenko ◽  
Rachel M. Sherman ◽  
Roman Petrovski ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Structural Variations ◽  
Short Read ◽  
Three Samples ◽  
Genomics Research ◽  
Long Read ◽  
Short Read Sequence ◽  
Population Scale

AbstractAccurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical sequencing pipelines. We introduce Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations. We demonstrate the accuracy of Paragraph on whole-genome sequence data from three samples using long read SV calls as the truth set, and then apply Paragraph at scale to a cohort of 100 short-read sequenced samples of diverse ancestry. Our analysis shows that Paragraph has better accuracy than other existing genotypers and can be applied to population-scale studies.

scholarly journals Comprehensive analysis of GBA using a novel algorithm for Illumina whole-genome sequence data or targeted Nanopore sequencing

2021 ◽  
Author(s):  
Marco Toffoli ◽  
Xiao Chen ◽  
Fritz J Sedlazeck ◽  
Chiao-Yin Lee ◽  
Stephen Mullin ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Short Read ◽  
Increased Risk ◽  
Long Read

GBA variants cause the autosomal recessive Gaucher disease, and carriers are at increased risk of Parkinson disease (PD) and Lewy body dementia (LBD). The presence of a highly homologous nearby pseudogene (GBAP1) predisposes to a range of structural variants arising from either gene conversion or reciprocal recombination, the latter resulting in copy number gains or losses, complicating genetic testing and analysis. To date, short-read sequencing has not been able to fully resolve these or other variants in the key homology region, and targeted long-read sequencing has not previously resolved reciprocal recombinants. We present and validate two independent methods to resolve recombinant alleles and other variants in GBA: Gauchian, a novel bioinformatics tool for short-read, whole-genome sequencing data analysis, and Oxford Nanopore long-read sequencing after enrichment with appropriate PCR. The methods were concordant for 42 samples including 30 with a range of recombinants and GBAP1-related mutations, and Gauchian outperforms the GATK Best Practices pipeline. Applying Gauchian to Illumina sequencing of over 10,000 individuals from publicly available cohorts shows that copy number variants (CNVs) spanning GBAP1 are relatively common in Africans. CNV frequencies in PD and LBD are similar to controls, but gains may coexist with other mutations in patients, and a modifying effect cannot be excluded. Gauchian detects a higher frequency of GBA variants in LBD than PD, especially severe ones. These findings highlight the importance of accurate GBA mutation detection in these patients, which is possible by either Gauchian analysis of short-read whole genome sequencing, or targeted long-read sequencing.

Improving Sample Preparation Methods For Cannabis-Infused Edible And Topical Products

Planta Medica ◽  
2016 ◽  
Vol 82 (05) ◽  
Author(s):  
M Wilcox ◽  
M Jacyno ◽  
J Marcu ◽  
J Neal-Kababick
Keyword(s):  
Sample Preparation ◽  
Preparation Methods ◽  
Sample Preparation Methods

Thin-Die Flip Chip Physical-FA Process Flow

2002 ◽  
Author(s):  
Andrew J. Komrowski ◽  
N. S. Somcio ◽  
Daniel J. D. Sullivan ◽  
Charles R. Silvis ◽  
Luis Curiel ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Failure Analysis ◽  
Flip Chip ◽  
Semiconductor Industry ◽  
Organic Substrate ◽  
Fault Isolation ◽  
Preparation Methods ◽  
Chip Technology ◽  
Isolation Test ◽  
Sample Preparation Methods

Abstract The use of flip chip technology inside component packaging, so called flip chip in package (FCIP), is an increasingly common package type in the semiconductor industry because of high pin-counts, performance and reliability. Sample preparation methods and flows which enable physical failure analysis (PFA) of FCIP are thus in demand to characterize defects in die with these package types. As interconnect metallization schemes become more dense and complex, access to the backside silicon of a functional device also becomes important for fault isolation test purposes. To address these requirements, a detailed PFA flow is described which chronicles the sample preparation methods necessary to isolate a physical defect in the die of an organic-substrate FCIP.

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