scholarly journals Evaluation of analytical protocols of alignment mapping tools using high throughput next-generation genome sequencing data

2021 ◽  
Vol 3 (1) ◽  
pp. 61
Author(s):  
Artur Bąk ◽  
Dawid Bodziony ◽  
Grzegorz Migdałek ◽  
Chandra Shekhar Pareek ◽  
Kacper Żukowski
Keyword(s):  
Genome Sequencing ◽  
High Throughput ◽  
Next Generation ◽  
Sequencing Data ◽  
Analytical Protocols

scholarly journals Detection of identity by descent using next-generation whole genome sequencing data

2012 ◽  
Vol 13 (1) ◽  
Author(s):  
Shu-Yi Su ◽  
Jay Kasberger ◽  
Sergio Baranzini ◽  
William Byerley ◽  
Wilson Liao ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Next Generation ◽  
Sequencing Data ◽  
Identity By Descent

scholarly journals A High-Throughput Skim-sequencing Approach for Genotyping, Dosage Estimation and Identifying Translocations

2021 ◽  
Author(s):  
Laxman Adhikari ◽  
Sandesh Shrestha ◽  
Shuanyge Wu ◽  
Jared Crain ◽  
Liangliang Gao ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
High Throughput ◽  
Low Cost ◽  
Introgression Lines ◽  
Whole Genome ◽  
Sequencing Data ◽  
Genomic Libraries ◽  
Genetics Research ◽  
Large Populations ◽  
Sequencing Platforms

Abstract The development of next generation sequencing (NGS) enabled a shift from array-based genotyping to high-throughput genotyping by directly sequencing genomic libraries. Even though whole genome sequencing was initially too costly for routine analysis in large populations, such as those utilized for breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to utilize whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage, a limitation comes in the time and high cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on amount of data required and extended to 3,072 samples or more. Panels of double haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T. aestivum x Hordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1x down to 0.01x per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the low coverage skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

scholarly journals Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

2015 ◽  
Vol 53 (5) ◽  
pp. 1685-1692 ◽  
Author(s):  
Shaokang Zhang ◽  
Yanlong Yin ◽  
Marcus B. Jones ◽  
Zhenzhen Zhang ◽  
Brooke L. Deatherage Kaiser ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
High Throughput ◽  
Sequencing Data ◽  
Salmonella Serotype

scholarly journals Overview of Genomic Tools for Circular Visualization in next-Generation Genomic Sequencing Era

2018 ◽  
Author(s):  
Alisha Parveen ◽  
Sukank Khurana ◽  
Abhishek Kumar
Keyword(s):  
Human Genome ◽  
Genome Sequencing ◽  
Genomic Sequencing ◽  
Next Generation ◽  
Sequencing Data ◽  
The Third ◽  
Genomic Tools ◽  
Rapid Changes ◽  
Human Genome Sequencing ◽  
Visualization Tools

After human genome sequencing and rapid changes in genome sequencing methods, we have entered in the era of rapidly accumulating genome-sequencing data. This has poses development of several types of methods for representing results of genome sequencing data. Circular genome visualizations tools are also critical in this area as they provide rapid interpretation and simple visualization of overall data. In the last 15 years, we have seen rapid changes in circular visualization tools after the development of the circos tool with 1–2 tools published per year. Herein we have summarized and revisited all these tools until the third quarter of 2018. 

scholarly journals A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ulrike Frank ◽  
Susanne Kublik ◽  
Dörte Mayer ◽  
Marion Engel ◽  
Michael Schloter ◽  
...  
Keyword(s):  
Cell Death ◽  
Next Generation Sequencing ◽  
Genome Sequencing ◽  
High Throughput ◽  
Target Enrichment ◽  
Next Generation ◽  
Mutant Screen ◽  
Specific Target ◽  
Dna Insertion ◽  
Generation Sequencing

Abstract Background Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death. Results Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO2 fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO2 whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO2. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO2-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation. Conclusions The presented NO2 dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.

scholarly journals Development and Validation of a High-Throughput Next-Generation Sequencing Workflow for SARS-CoV-2 Whole Genome Sequencing: Results from Over 65,000 Clinical Cases

2021 ◽  
Author(s):  
Sun Hee Rosenthal ◽  
Anna Gerasimova ◽  
Rolando Ruiz-Vega ◽  
Kayla Livingston ◽  
Ron M. Kagan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
High Throughput ◽  
The United States ◽  
Primer Binding Site ◽  
Whole Genome ◽  
Next Generation ◽  
Pcr Method ◽  
Generation Sequencing

Abstract Monitoring new mutations in SARS-CoV-2 provides crucial information for identifying diagnostic and therapeutic targets and important insights to achieve a more effective COVID-19 control strategy. Next generation sequencing (NGS) technologies have been widely used for whole genome sequencing of SARS-CoV-2. While various NGS methods have been reported, one chief limitation has been the complexity of the workflow, limiting the scalability. Here, we overcome this limitation by designing a workflow optimized for high-throughput studies. The workflow utilizes modified ARTIC network v3 primers for SARS-CoV-2 whole genome amplification. NGS libraries were prepared by a 2-step PCR method, similar to a previously reported tailed PCR method, with further optimizations to improve amplicon balance, to minimize amplicon dropout for viral genomes harboring primer-binding site mutation(s), and to integrate robotic liquid handlers. Validation studies demonstrated that the optimized workflow can process up to 2,688 samples in a single sequencing run without compromising sensitivity and accuracy and with fewer amplicon dropout events compared to the standard ARTIC protocol. We additionally report results for over 65,000 SARS-CoV-2 whole genome sequences from clinical specimens collected in the United States between January and September of 2021, as part of an ongoing national genomics surveillance effort.

scholarly journals A REVIEW ON NEXT-GENERATION SEQUENCING SAMPLE PREPARATION

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
A. K. Gupta
Keyword(s):  
Next Generation Sequencing ◽  
Sample Preparation ◽  
Genome Sequencing ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Test Procedure ◽  
Next Generation ◽  
Specialized Exhibition ◽  
Generation Sequencing

To stay aware of interest for sample arrangement, numerous high-throughput sequencing labs have computerized specimen arrangement strategies. The point when selecting a robotization stage, clients might as well recognize the specialized exhibition of the fluid handler and its demonstrated exhibition for NGS test procedure. NGS test arrangement stages may as well offer clients a critical decrease in involved time and the adaptability to run numerous methodologies. In light of the fact that the sample readiness protocol for NGS are quickly developing, a perfect robotization framework ought to be good with reagents for different requirements on advancing sequencing stages.Key words: NGS, genome sequencing, BenchCel Workstation, Benchbot Robot, Bravo platform, automation protocols

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