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1. Full Text ANGSD: Analysis of Next Generation Sequencing Data
by Korneliussen, Thorfinn Sand and Albrechtsen, Anders and Nielsen, Rasmus
BMC Bioinformatics, ISSN 1471-2105, 11/2014, Volume 15, Issue 1, pp. 356 - 356
Background: High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in... 
Association studies | Next-generation sequencing | Bioinformatics | Population genetics | ACCURATE | GENOTYPE | STATISTICS | BIOCHEMICAL RESEARCH METHODS | SHORT READ ALIGNMENT | NGS DATA | DISCOVERY | GENOME SEQUENCE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | FRAMEWORK | ASSOCIATION | HISTORY | Likelihood Functions | Genetics, Population - methods | Gene Frequency | Genotype | Polymorphism, Single Nucleotide | Software | High-Throughput Nucleotide Sequencing - methods | Genetic aspects | Nucleotide sequencing | Analysis | DNA sequencing | Genotype & phenotype | Genomes | C plus plus | Chromosomes | Index Medicus | Freeware | Format | Statistical analysis | Samples | Statistical methods | Source code | Statistics | Sequencing
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2. Full Text ACMG clinical laboratory standards for next-generation sequencing
by Rehm, Heidi L and Bale, Sherri J and Bayrak-Toydemir, Pinar and Berg, Jonathan S and Brown, Kerry K and Deignan, Joshua L and Friez, Michael J and Funke, Birgit H and Hegde, Madhuri R and Lyon, Elaine and Amer Coll Med Genetics and Genomics Lab Quality Assurance and Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee and for the Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee
Genetics in Medicine, ISSN 1098-3600, 09/2013, Volume 15, Issue 9, pp. 733 - 747
Next-generation sequencing technologies have been and continue to be deployed in clinical laboratories, enabling rapid transformations in genomic medicine.... 
standards | genome sequencing | guidelines | ACMG | exome sequencing | next-generation sequencing | EXOME | RECOMMENDATIONS | GENETICS & HEREDITY | FRAMEWORK | GENOME | Laboratories - standards | Reproducibility of Results | Genetic Testing - standards | United States | Humans | Translational Medical Research | Sequence Analysis, DNA - standards | High-Throughput Nucleotide Sequencing - standards | Exome | Sequence Analysis, DNA - instrumentation | Genome, Human | Genomics - methods | Sequence Analysis, DNA - methods | Index Medicus
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3. Full Text Targeted Next‐Generation Sequencing can Replace Sanger Sequencing in Clinical Diagnostics
by Sikkema‐Raddatz, Birgit and Johansson, Lennart F and Boer, Eddy N and Almomani, Rowida and Boven, Ludolf G and Berg, Maarten P and Spaendonck‐Zwarts, Karin Y and Tintelen, J. Peter and Sijmons, Rolf H and Jongbloed, Jan D. H and Sinke, Richard J
Human Mutation, ISSN 1059-7794, 07/2013, Volume 34, Issue 7, pp. 1035 - 1042
Mutation detection through exome sequencing allows simultaneous analysis of all coding sequences of genes. However, it cannot yet replace S anger sequencing (... 
targeted | guidelines | diagnostics | NGS | next‐generation sequencing | Targeted NGS | Next-generation sequencing | Diagnostics | Guidelines | next-generation sequencing | GENETICS & HEREDITY | DILATED CARDIOMYOPATHY | targeted NGS | CAPTURE | Cardiomyopathy, Dilated - genetics | Cardiomyopathies - genetics | Reproducibility of Results | Exons | Humans | Sensitivity and Specificity | Cardiomyopathies - diagnosis | Cardiomyopathy, Dilated - diagnosis | Mutation | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | Nucleotide sequencing | Diagnostic equipment (Medical) | Media coverage | DNA sequencing | Cardiomyopathy | Index Medicus
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4. Full Text High-throughput next-generation sequencing of polioviruses
by Montmayeur, Anna M and Ng, Terry Fei Fan and Schmidt, Alexander and Zhao, Kun and Magaña, Laura and Iber, Jane and Castro, Christina J and Chen, Qi and Henderson, Elizabeth and Ramos, Edward and Shaw, Jing and Tatusov, Roman L and Dybdahl-Sissoko, Naomi and Endegue-Zanga, Marie Claire and Adeniji, Johnson A and Oberste, M. Steven and Burns, Cara C
Journal of Clinical Microbiology, ISSN 0095-1137, 02/2017, Volume 55, Issue 2, pp. 606 - 615
The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is... 
Picornavirus | Cell culture | Metagenomics | Next-generation sequencing | FTA cards | Poliovirus | cell culture | next-generation sequencing | GLOBAL POLIO ERADICATION | GENOMES | metagenomics | SURVEILLANCE | MICROBIOLOGY | IDENTIFICATION | picornavirus | poliovirus | Pilot Projects | Humans | Specimen Handling - methods | Poliovirus - genetics | Poliovirus - classification | High-Throughput Nucleotide Sequencing - methods | Molecular Epidemiology - methods | Index Medicus | Virology
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5. Full Text Ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
by Shen, Li and Shao, Ningyi and Liu, Xiaochuan and Nestler, Eric
BMC Genomics, ISSN 1471-2164, 04/2014, Volume 15, Issue 1, pp. 284 - 284
Background: Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to... 
Visualization | Genomic databases | Epigenomics | Next-generation sequencing | Data mining | DNA METHYLATION | CHROMATIN | TRANSCRIPTION | RNA-SEQ EXPERIMENTS | TET PROTEINS | GENE | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | EMBRYONIC STEM-CELLS | GENETICS & HEREDITY | R PACKAGE | 5-HYDROXYMETHYLCYTOSINE | EXPRESSION | Embryonic Stem Cells - metabolism | Promoter Regions, Genetic | Computational Biology - methods | Reproducibility of Results | Humans | Databases, Genetic | Workflow | Sequence Analysis, RNA - methods | Algorithms | Animals | Epigenomics - methods | High-Throughput Nucleotide Sequencing | Software | Genomics - methods | Sequence Analysis, DNA - methods | Data Mining - methods | Web Browser | Research | Nucleotide sequencing | Innovations | DNA sequencing | Proteins | Visualization (Computers) | Design | DNA methylation | Genomes | Gene expression | Programming languages | Data bases | Index Medicus
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6. Full Text Cell-Free DNA Next-Generation Sequencing in Pancreatobiliary Carcinomas
by Zill, Oliver A and Greene, Claire and Sebisanovic, Dragan and Siew, Lai Mun and Leng, Jim and Vu, Mary and Hendifar, Andrew E and Wang, Zhen and Atreya, Chloe E and Kelley, Robin K and Van Loon, Katherine and Ko, Andrew H and Tempero, Margaret A and Bivona, Trever G and Munster, Pamela N and Talasaz, Amirali and Collisson, Eric A
Cancer Discovery, ISSN 2159-8274, 10/2015, Volume 5, Issue 10, pp. 1040 - 1048
Patients with pancreatic and biliary carcinomas lack personalized treatment options, in part because biopsies are often inadequate for molecular... 
Pancreatic Neoplasms - blood | Carcinoma - blood | Reproducibility of Results | Prognosis | Pancreatic Neoplasms - diagnosis | Humans | Gene Expression Profiling - methods | Mutation Rate | Pancreatic Neoplasms - genetics | Biomarkers, Tumor | Disease Progression | Bile Duct Neoplasms - diagnosis | Bile Duct Neoplasms - therapy | DNA, Neoplasm - blood | Sensitivity and Specificity | Carcinoma - genetics | High-Throughput Nucleotide Sequencing | Bile Duct Neoplasms - blood | Bile Duct Neoplasms - genetics | DNA, Neoplasm - genetics | Mutation | Neoplasm Staging | Pancreatic Neoplasms - therapy | Index Medicus | cell-free DNA | pancreatic adenocarcinoma | next-generation sequencing | cholangiocarcinoma | circulating tumor DNA
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7. Full Text Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads
by Jiang, Hongshan and Lei, Rong and Ding, Shou-Wei and Zhu, Shuifang
BMC Bioinformatics, ISSN 1471-2105, 06/2014, Volume 15, Issue 1, pp. 182 - 182
Background: Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA... 
Approximate string matching | Adapter trimming | Next generation sequencing | Barcode demultiplexing | Local sequence alignment | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | IDENTIFICATION | TOOL | Caenorhabditis elegans | Algorithms | Animals | Sequence Analysis, RNA | Time Factors | Arabidopsis | Drosophila | Humans | Software | High-Throughput Nucleotide Sequencing - methods | RNA sequencing | Genomes | Dynamic programming | Genetic testing | Deoxyribonucleic acid--DNA | Index Medicus
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8. Full Text Applications of next-generation sequencing in plant biology
by Ashley N. Egan and Jessica Schlueter and David M. Spooner
American Journal of Botany, ISSN 0002-9122, 2/2012, Volume 99, Issue 2, pp. 175 - 185
The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS... 
Introduction | genomics | plant biology | development | next‐generation sequencing | DNA sequencing | Development | Plant biology | Next-generation sequencing | Genomics | next-generation sequencing | ENRICHMENT STRATEGIES | CHALLENGES | GALAXY | PLANT SCIENCES | BIOINFORMATICS | RNA-SEQ | GENES | REVEALS | Polyploidy | Computational Biology | Databases, Genetic | Magnoliopsida - genetics | Genome, Plant | Phylogeny | Sequence Analysis, RNA - methods | Hybridization, Genetic | Ecosystem | Sensitivity and Specificity | Polymorphism, Single Nucleotide | Chromosomes, Plant - genetics | Magnoliopsida - classification | Sequence Analysis, DNA - methods | DNA, Plant - genetics | Microsatellite Repeats | Phylogenetics | Genetic markers | Deoxyribonucleic acid--DNA | Index Medicus
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9. Full Text Next-Generation Sequencing of Infectious Pathogens
by Gwinn, M and MacCannell, D and Armstrong, GL
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION, ISSN 0098-7484, 03/2019, Volume 321, Issue 9, pp. 893 - 894
The use and importance of next-generation sequencing for the diagnosis of pathogens is discussed. The next-generation sequencing techniques allow improvement... 
MEDICINE, GENERAL & INTERNAL | TECHNOLOGIES | Usage | Control | Disease transmission | Microbiology | Communicable diseases | Genetic aspects | Diagnosis | Nucleotide sequencing | Research | DNA sequencing | Pathogens | Next-generation sequencing | Antimicrobial resistance | Virulence | Index Medicus | Abridged Index Medicus
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10. Full Text AdapterRemoval: Easy cleaning of next-generation sequencing reads
by Lindgreen, Stinus
BMC Research Notes, ISSN 1756-0500, 2012, Volume 5, Issue 1, pp. 337 - 337
With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One... 
Next-generation sequencing | Data pre-processing | Paired-end reads | Adapter trimming | Sequence alignment | Single-end reads | Sequence Analysis, DNA - instrumentation | Polymorphism, Single Nucleotide | Algorithms | Nucleotides | Nucleotide sequencing | Single nucleotide polymorphisms | Analysis | DNA sequencing | Problems | Genomes | Colleges & universities | Index Medicus
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11. Full Text Next generation sequencing in clinical diagnosis
by Lee, Hane and Martinez-Agosto, Julian A and Rexach, Jessica and Fogel, Brent L
The Lancet Neurology, ISSN 1474-4422, 05/2019, Volume 18, Issue 5, pp. 426 - 426
Medical diagnosis | Laboratories | Next-generation sequencing
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12. Full Text Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
by Kong, Yong
Genomics, ISSN 0888-7543, 2011, Volume 98, Issue 2, pp. 152 - 153
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It... 
Bit-vector algorithm | Next-generation sequencing | Barcode assignment | Approximate string matching | Adapters trimming | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | Software | Algorithms | High-Throughput Nucleotide Sequencing - methods | Sequence Analysis, DNA - methods | Fighter planes | Index Medicus
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13. Full Text Quantifying population genetic differentiation from next-generation sequencing data
by Fumagalli, Matteo and Vieira, Filipe G and Korneliussen, Thorfinn Sand and Linderoth, Tyler and Huerta-Sánchez, Emilia and Albrechtsen, Anders and Nielsen, Rasmus
Genetics, ISSN 0016-6731, 2013, Volume 195, Issue 3, pp. 979 - 992
Over the past few years, new high-throughput DNA sequencing technologies have dramatically increased speed and reduced sequencing costs. However, the use of... 
next-generation sequencing | PRINCIPAL COMPONENT ANALYSIS | F-ST | MARKERS | LOCI | INFERENCE | principal components analysis | GENETICS & HEREDITY | GENOME VARIATION | SELECTION | ASSOCIATION | MAP | ESTIMATING F-STATISTICS | REVEALS | Data Interpretation, Statistical | Genetic Drift | Computational Biology | Selection, Genetic | Genotype | Bombyx - genetics | High-Throughput Nucleotide Sequencing - statistics & numerical data | Genetic Variation | Likelihood Functions | Animals | Computer Simulation | Models, Genetic | Mutation | Principal Component Analysis | Genetics, Population - statistics & numerical data | Measurement | Usage | Genetic variation | Nucleotide sequencing | Research | Population genetics | DNA sequencing | Cellular biology | Deoxyribonucleic acid--DNA | Index Medicus | F ST | Investigations
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14. Full Text A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
by Quail, Michael A and Smith, Miriam and Coupland, Paul and Otto, Thomas D and Harris, Simon R and Connor, Thomas R and Bertoni, Anna and Swerdlow, Harold P and Gu, Yong
BMC Genomics, ISSN 1471-2164, 07/2012, Volume 13, Issue 1, pp. 341 - 341
Background: Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three... 
GC-rich | Next-generation sequencing | Pacific biosciences | Bias | PGM | SMRT | Ion torrent | AT-rich | Illumina | MiSeq | Genome coverage | AMPLIFICATION-FREE | LIBRARIES | GENOME SEQUENCE | ALIGNMENT | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | SEQ | Staphylococcus aureus - genetics | Gene Library | Nucleotide Motifs - genetics | Bordetella pertussis - genetics | Databases, Genetic | Genome, Bacterial - genetics | Sequence Analysis, DNA - instrumentation | Base Sequence | Plasmodium falciparum - genetics | Polymorphism, Single Nucleotide - genetics | Genome, Protozoan - genetics | Base Composition - genetics | Sequence Analysis, DNA - methods | Usage | DNA sequencers | Nucleotide sequencing | Comparative analysis | Methods | DNA sequencing | Plasmodium falciparum | Malaria | Genomics | Hostages | Genomes | Instrument industry | Silicon wafers | Real time | Price quotations | Index Medicus
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