The impact of next-generation sequencing on genomics

“Following completion of the HGP, a new approach, genome-wide association study (GWAS), was widely applied to genomics.”

“The core philosophy of massive parallel sequencing used in next-generation sequencing (NGS) is adapted from shotgun sequencing (Venter et al., 2003; Margulies et al., 2005; Shendure et al., 2005).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“Sanger sequencing was used to obtain the first consensus sequence of the human genome in 2001 (Lander et al., 2001; Venter et al., 2001) and the first individual human diploid sequence (J. Craig Venter) in 2007 (Levy et al., 2007).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”

“Individual human genomes (one Asian and one African) have been successfully sequenced and assembled using the Illumina Genome Analyzer (read lengths ranged from 35 to 75 basepairs) with a modified SOAP program, SOAPdenovo (Li et al., 2010).”

“SIFT (Sorting Intolerant From Tolerant) is used to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of the amino acid can be applied to find non-synonymous polymorphisms within NGS data (Ng and Henikoff, 2001,2002).”

“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”

“Nano-technologies have long been considered a cutting-edge technology for single-molecule DNA sequencing (Iqbal et al., 2007; Branton et al., 2008) and several nanopore sequencing concepts and technologies are currently under development.”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“Polymorphism Phenotyping (PolyPhen) and updated PolyPhen-2 are tools which predict the possible impact of an amino acid substitution on the structure and function of a specific protein using straightforward comparative physical methods (Sunyaev et al., 2001;Ramensky et al., 2002).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“…strategy, the mutations in DHODH from four individuals from three unrelated families with Miller syndrome have been successfully identified (Ng et al., 2010a), illustrating that selective DNA enrichment techniques will dramatically reduce overall cost and accelerate discovery of genetic…”

“Shortly thereafter, the second complete individual genome (James D. Watson) was sequenced using next-generation technology, which marked the first human genome sequenced with new NGS technology (Wheeler et al., 2008).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Sanger sequencing was used to obtain the first consensus sequence of the human genome in 2001 (Lander et al., 2001; Venter et al., 2001) and the first individual human diploid sequence (J. Craig Venter) in 2007 (Levy et al., 2007).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“The core philosophy of massive parallel sequencing used in next-generation sequencing (NGS) is adapted from shotgun sequencing (Venter et al., 2003; Margulies et al., 2005; Shendure et al., 2005).”

“…strategy, the mutations in DHODH from four individuals from three unrelated families with Miller syndrome have been successfully identified (Ng et al., 2010a), illustrating that selective DNA enrichment techniques will dramatically reduce overall cost and accelerate discovery of genetic…”

“Such rare variants may have a large effect as genetic risk factors for complex genetic diseases (Frazer et al., 2009; Manolio et al., 2009; Schork et al., 2009; Tsuji, 2010).”

“Polymorphism Phenotyping (PolyPhen) and updated PolyPhen-2 are tools which predict the possible impact of an amino acid substitution on the structure and function of a specific protein using straightforward comparative physical methods (Sunyaev et al., 2001;Ramensky et al., 2002).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“Predictor of human Deleterious Single Nucleotide Polymorphisms (PhD-SNP) is an optimized program to predict if a given single point protein mutation can be classified as disease-related or as neutral polymorphism based on protein sequence and profile information (Capriotti et al., 2006).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“It is a challenge to efficiently align short reads to a reference genome, especially when developing new algorithms to handle ambiguities or lack of accuracy during the alignment (Li and Homer, 2010).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“Currently de novo assembly with NGS data is generally limited to microbial genome projects (Metagenomics) due to the small bacterial genome size (Chistoserdova, 2010; Wooley et al., 2010).”

“SIFT (Sorting Intolerant From Tolerant) is used to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of the amino acid can be applied to find non-synonymous polymorphisms within NGS data (Ng and Henikoff, 2001,2002).”

“Following completion of the HGP, a new approach, genome-wide association study (GWAS), was widely applied to genomics.”

“CloudBurst is another new parallel read-mapping cloud algorithm optimized for mapping NGS data to a human reference genome, SNP discovery, genotyping and personal genomics (Schatz, 2009).”

“More detailed technical description of these platforms are available elsewhere (Mardis, 2008a,b, 2009; Schuster, 2008; Shendure and Ji, 2008; Ansorge, 2009; Harismendy et al., 2009; Tucker et al., 2009; Voelkerding et al., 2009; Metzker, 2010; Ng and Kirkness, 2010).”

“…detection software, which includes screening genomes for structural and single nucleotide variants and the differences between genomes (Li et al., 2009; Medvedev et al., 2009; Thusberg and Vihinen, 2009), are generally integrated with alignment and assembly processes and are listed in Table 4.”

“The full benefit of NGS will not be achieved until bioinformatics are able to maximally interpret and utilize these short-read sequences, including alignment, assembly, etc (Pop and Salzberg, 2008).”

“Other genetic loci for rare diseases have also been successfully identified through exome sequencing (Bilguvar et al., 2010; Ng et al., 2010a,b; Rios et al., 2010; Walsh et al., 2010), further validating this strategy.”

“CrossBow is the first cloud computing software capable of performing alignment and single nucleotide polymorphism analysis on multiple whole-human datasets (Langmead et al., 2009).”

“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”

“Nano-technologies have long been considered a cutting-edge technology for single-molecule DNA sequencing (Iqbal et al., 2007; Branton et al., 2008) and several nanopore sequencing concepts and technologies are currently under development.”

“By considering the physiochemical variations presented in protein sequence alignment and the property of variations, Multivariate Analysis of Protein Polymorphism (MAPP) can predict the impact of all possible amino acid substitutions on the function of the protein (Stone and Sidow, 2005).”

“As such, advanced single DNA molecule sequencing technology has been defined as the next-NGS technology (Pettersson et al., 2009).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“Targeted sequencing generally focuses on all protein-coding subsequences (the functional exome), which only requires ~5% as much sequencing compared to that required for the entire human genome (Pussegoda, 2010; Senapathy et al., 2010; Teer and Mullikin, 2010).”

“Other genetic loci for rare diseases have also been successfully identified through exome sequencing (Bilguvar et al., 2010; Ng et al., 2010a,b; Rios et al., 2010; Walsh et al., 2010), further validating this strategy.”

“The primary goal of current algorithms and computing for short-read assembly with NGS technologies is to increase read length (Chaisson et al., 2009).”

“A common strategy for NGS is to use DNA synthesis or ligation process to read through many different DNA templates in parallel (Fuller et al., 2009).”

“Although several early GWAS studies reported potentially promising results, the majority of GWAS studies were disappointing because of inadequate sample size, limitation of arrays for certain genetic variations, and/or heterogeneity in phenotype (Daly, 2010a).”

“There is no doubt that the progress of genomics will eventually lead to the birth of genetic medicine which will propel significant advances and improvements in human health (Gonzalez-Angulo et al., 2010).”

“The parallel short-read strategy of NGS opens many challenges for bioinformatics to interpret the short reads and the genetic variations in human genomes (Wold and Myers, 2008; Yang et al., 2009).”

“…detection software, which includes screening genomes for structural and single nucleotide variants and the differences between genomes (Li et al., 2009; Medvedev et al., 2009; Thusberg and Vihinen, 2009), are generally integrated with alignment and assembly processes and are listed in Table 4.”

“Several unique single-molecule DNA sequencing technologies are currently under development; however, little information has been made publically available (Gupta, 2008; Xu et al., 2009; Metzker, 2010; Treffer and Deckert, 2010).”

“…selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform coverage, high reproducibility, and…”

“By targeting specific regions of interest, selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform…”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“…1000 genome project the cost of sequencing an individual genome has been rapidly decreasing and will likely reach $1000 per person within a short period of time (von Bubnoff, 2008), making personalized medicine become a possible reality (Lunshof et al., 2010; Mardis, 2006; Harismendy et al., 2009).”

“Other genetic loci for rare diseases have also been successfully identified through exome sequencing (Bilguvar et al., 2010; Ng et al., 2010a,b; Rios et al., 2010; Walsh et al., 2010), further validating this strategy.”

“By targeting specific regions of interest, selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform…”

“At 600 bp, the 454 Sequencer has the longest short reads among all the NGS platforms; and generates ~400–600 Mb of sequence reads per run; critical for some applications such as RNA isoform identification in RNA-seq and de novo assembly of microbes in metagenomics (Mocali and Benedetti, 2010).”

“Efforts to date have focused on overcoming the limitation of short reads for genome-wide analysis, but unfortunately, current available bioinformatics ability and computing power is lagging far behind the needs for NGS sequencing data analysis (McPherson, 2009).”

“Some online utility programs, such as EagleView (Huang and Marth, 2008) or LookSeq (Manske and Kwiatkowski, 2009), also provide some additional assistance on NGS data analysis and interpretation (Table 3).”

“Several unique single-molecule DNA sequencing technologies are currently under development; however, little information has been made publically available (Gupta, 2008; Xu et al., 2009; Metzker, 2010; Treffer and Deckert, 2010).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“Although several early GWAS studies reported potentially promising results, the majority of GWAS studies were disappointing because of inadequate sample size, limitation of arrays for certain genetic variations, and/or heterogeneity in phenotype (Daly, 2010a).”

“In genomics, the personal genome era made available by NGS technologies will mark a significant milestone in entire genomic research field in the foreseeable future (Zhang and Dolan, 2010; Holmes et al., 2009).”

“Currently de novo assembly with NGS data is generally limited to microbial genome projects (Metagenomics) due to the small bacterial genome size (Chistoserdova, 2010; Wooley et al., 2010).”

“…1000 genome project the cost of sequencing an individual genome has been rapidly decreasing and will likely reach $1000 per person within a short period of time (von Bubnoff, 2008), making personalized medicine become a possible reality (Lunshof et al., 2010; Mardis, 2006; Harismendy et al., 2009).”

“…of heritability, indicating that GWAS based on the “common disease-common variants hypothesis” is not very effective in identifying genetic variants for complex traits, and common genetic variability is unlikely to explain the entire genetic predisposition to disease (Singleton et al., 2010).”

“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”

“Such rare variants may have a large effect as genetic risk factors for complex genetic diseases (Frazer et al., 2009; Manolio et al., 2009; Schork et al., 2009; Tsuji, 2010).”

“…overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform coverage, high reproducibility, and no allele bias for any genomic region (Stratton, 2008).”

“Several unique single-molecule DNA sequencing technologies are currently under development; however, little information has been made publically available (Gupta, 2008; Xu et al., 2009; Metzker, 2010; Treffer and Deckert, 2010).”

“Some online utility programs, such as EagleView (Huang and Marth, 2008) or LookSeq (Manske and Kwiatkowski, 2009), also provide some additional assistance on NGS data analysis and interpretation (Table 3).”

“…regions of interest, selective DNA enrichment techniques improve the overall cost and efficiency of NGS (Rehman et al., 2010; Volpi et al., 2010; Bau et al., 2009; Levin et al., 2009; Ng et al., 2009b; Ng and Kirkness, 2010); however, targeted enrichment must maintain uniform coverage, high…”

“The core philosophy of massive parallel sequencing used in next-generation sequencing (NGS) is adapted from shotgun sequencing (Venter et al., 2003; Margulies et al., 2005; Shendure et al., 2005).”

“The parallel short-read strategy of NGS opens many challenges for bioinformatics to interpret the short reads and the genetic variations in human genomes (Wold and Myers, 2008; Yang et al., 2009).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”

“The term “genomics” was used as the name of the first journal in the field of genomics (McKusick and Ruddle, 1987).”

“In genomics, the personal genome era made available by NGS technologies will mark a significant milestone in entire genomic research field in the foreseeable future (Zhang and Dolan, 2010; Holmes et al., 2009).”

“It is challenging to develop software with the ability to distinguish low-frequency alleles descendent from ancient ancestors from de novo or extremely rare mutations recently introduced into the population (Nakken et al., 2007; van Oeveren and Janssen, 2009).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“It is challenging to develop software with the ability to distinguish low-frequency alleles descendent from ancient ancestors from de novo or extremely rare mutations recently introduced into the population (Nakken et al., 2007; van Oeveren and Janssen, 2009).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“New genomic technologies have revolutionized our understanding of many genes or genomic regions involved in the pathogenesis of human diseases (Novelli et al., 2010).”

“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”

“Targeted sequencing generally focuses on all protein-coding subsequences (the functional exome), which only requires ~5% as much sequencing compared to that required for the entire human genome (Pussegoda, 2010; Senapathy et al., 2010; Teer and Mullikin, 2010).”

“Targeted sequencing generally focuses on all protein-coding subsequences (the functional exome), which only requires ~5% as much sequencing compared to that required for the entire human genome (Pussegoda, 2010; Senapathy et al., 2010; Teer and Mullikin, 2010).”

“Although available NGS technologies utilize quite diverse chemistry and base incorporation ⁄ detection tools, they share two main steps: library fragmentation ⁄ amplicon library preparation and detection of the incorporated nucleotides (Glenn 2011; Zhang et al. 2011).”

“Since the size of the data samples is constantly increasing [2, 3], Reactome offers a set of pathway analysis tools which aim to deal with this scenario and yet provide reliable and accurate results with interactive (seconds) response time for genome-wide datasets.”

“The tremendous progress in massively parallel sequencing technologies enables investigators to efficiently obtain genetic information down to single base resolution on a genome-wide scale [1, 2, 3].”

“The agent is able to (1) provide an interface for DICOM, HL7, HTTP, and XDS standard and nonstandardized data; (2) synchronize metadata on local PACS and RIS; (3) cache images and data received from local PACS, RIS, any input tool, or another agent; (4) archive image data with compression and multitier storage, backup…”

“NGS is a promising method for miRNA studies as it has major advantages in comparison to microarrays, including higher sensitivity, wider miRNA spectrum that can be analysed and the ability of de novo sequencing of so far unknown miRNAs.(22,23) We could demonstrate that MP contain a significantly distinct miRNA pattern…”

“Recently, access to detailed genomic information of animals by using next-generation sequencing has become easier [Zhang et al., 2011].”

“A detailed description of second generation sequencing platforms and principles can be found in dedicated reviews (e.g., Voelkerding et al., 2009; Metzker, 2010; Glenn, 2011; Pareek et al., 2011; Zhang et al., 2011; Liu et al., 2012; Shokralla et al., 2012; Mardis, 2013; Morey et al., 2013).”

“Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances.”

“Recently, with the development of the next-generation sequencing (NGS) (Behjati and Tarpey, 2013) more genes of different organisms have been sequenced and their gene elements have been computationally explored (Zhang et al., 2011).”

“It produces a massively parallel analysis from multiple samples where small sections of DNA are ligated with adaptors for random reads during DNA amplification which provides enormous data within a short duration (Zhang et al., 2011).”

“Furthermore, the types of error can be influenced by the characteristics of different sequencing technologies 7,8 .”

“The continuous and dynamic development of NGS represents an unprecedented opportunity for metagenomic applications, and is expanding our capacity to analyse microbial communities from a variety of habitats and environments [3,11].”

“The microbial genomics today has progressed from the long drawnout individual genome sequencing projects in the past to a level of technological advancement, where sequencing and comparing the genomes of several strains of a single pathogen is accomplished in a very short period of time [1, 2].”

“The appropriate value for a SNP threshold is context-specific and will be affected by study-specific factors such as strain diversity in the setting [31, 43] , the definition of a quality read, the extent of within-host diversity [15, 22, 25, 31, 38] and the number of amplification steps [1, [44] [45] [46] [47] (Addit…”

“One of the most important applications of NGS is to identify mutations, including single nucleotide polymorphisms (SNP), small insertions/deletions (INDELs), structural variations, e.g., translocations, inversions, and copy number variations (CNV) (Zhang et al., 2011; Bahassi el and Stambrook, 2014; Wadapurkar and Vya…”

“This platform generates the best data quality as a result of its sequencing-by-ligation approach (Zhang et al. 2011).”

“These technologies now allow for the parallel sequencing of millions of nucleotide sequences simultaneously (Wang et al., 2009; Zhang et al., 2011).”

“Transcriptome sequencing was conducted using a combination of 454 and Illumina technologies (Zhang et al. 2011).”

“, Illumina’s HiSeq200 V3 chemistry kit) (Clark et al., 2011; Zhang et al., 2011).”

“Raw sequencing reads were initially processed with GenomeQuest tools [12].”

“Aside from sequencing entire genomes—an approach that is becoming increasingly feasible (Allendorf et al. 2010; Seeb et al. 2011; Zhang et al. 2011)—the use of DNA markers to amplify random genomic regions remains the most accessible and widely used method of elucidating the distribution of genetic…”

“Advancement in molecular profiling technologies have enabled rapid whole genome sequencing, with better resolution that provides researchers the opportunity to scan for known genomic mutations, as well as identify novel genomic aberrations specific to different subsets of gastric carcinoma patients (26-28).”

“They divided the LAB species into two groups, where group I included the families Enterococcaceae and Streptococcaceae; within this group the monophyly of the genera Enterococcus, Lactococcus and Streptococcus were strongly supported (Zhang et al., 2011).”

“(2014), new introgression lines with high yields and fiber quality were developed as a result of interspecific hybridization between G. hirsutum and G. barbadense (Zhang, 2011).”

“007, Helicos Heliscope, and the system of Pacific Biosystems (reviewed by Metzker 2010; Zhang et al. 2011).”

“Although available platforms utilise quite diverse chemistry and base incorporation/detection tools, they all share two main steps: library preparation (fragmentation or amplicon preparation); and detection of the incorporated nucleotide (Zhang et al. 2011).”

“Consequently, these technologies have reached unprecedented levels of acceptance and implementation and are actively replacing classical technologies, such as Sanger sequencing, hybridization-based arrays, fluorescence in situ hybridization, qualitative real-time PCR, and PCR-coupled with fragment analysis platforms […”

“gonucleotides of the complementary probe that hybridize to the primer (Zhang et al., 2011).”

“Next-generation DNA sequencing technologies have accelerated the sequencing process, decreased the cost, and opened new horizons in the environmental understanding (Zhang et al., 2011).”

“This is due to the short length of the sequenced variable regions, typically at the level of genus at most [91], and precludes distinguishing between closely related species [92,93].”

“Second generation high-throughput DNA sequencing platforms such as Roche 454, SOLID and Illumina combined with the development of de novo assembly strategies have become powerful tools in transcriptomic studies for non-model organisms without a proper reference genome, and allow targeted identification of genes which…”

“For example, modern Illumina systems can generate several hundreds of gigabases per run (Zhang et al., 2011) with a high accuracy.”

“For all these reasons, and aided by extraordinary advances in genome sequencing facilities [16,17], there has been a tremendous effort to pursue the sequencing of filamentous fungi.”

“With the rapid development of novel technologies, there are a number of assays that can be considered and these have been reviewed elsewhere (Krueger et al. 2012; Zhou et al. 2011; Zhang et al. 2011; Ku et al. 2011).”

“As a matter of fact, due to the advances in genome sequencing technologies [6, 7], these methods represent the only practical strategy to keep up with the rapid accumulation of sequence information [8, 9].”

“Rapidly evolving sequencing technologies have exponentially increased the output of genomics data (1, 2), which has led to revolutionary discoveries in cancer biology and other biological sciences (3–5).”

“Recent improvements in next generation sequencing technologies (e.g. Zhang et al. 2011) have made the study of nonmodel organisms’ genomes more accessible, allowing for the first time the evaluation of multiple aspects of their genomic variation (e.g. Nekrutenko & Taylor 2012).”

“sativa, thereafter, new reference sequences from additional rice cultivars are needed, although chromosomal mapping and de novo assembly of the NGS reads are still challenging.(21,22) RicecultivarKasalathbelongsto the indica subspecies or aus group of O.”

“Rapidly evolving sequencing technologies [1,2] have led to a dramatic rise in the number of published articles reporting associations between genomic variations and diseases.”

“Next generation sequencing (NGS) provides large sequencing datasets at a fast sequencing speed and more lately at an affordable price [20].”

“For nonmodel species, de novo assembly presents additional challenges for SNP discovery and genotyping including spurious SNP calls as a result of collapsing paralogs into unique loci (Zhang et al. 2011).”

“These novel technologies generate a massive throughput at a considerably lower per base cost than traditional Sanger sequencing, and obviate the need for laborious cloning procedures [6–8].”

“The florescent light signals were detected by the Genome Analyzer, which performed basecalling [20].”

“Raw sequencing reads were initially processed with GenomeQuest tools [28].”

“…variants and quantification of gene expression (Meijer et al. 2005; Aanes et al. 2011; Coppe et al. 2010; Fu et al. 2011; Vesterlund et al. 2011; Zhang et al. 2011b), other applications such as SNP identification (Canovas et al. 2010; Yang et al. 2011), allele-specific gene expression (Degner…”

“NGS technologies now allow large quantities of high-quality DNA sequence data to be generated at modest cost (Zhang et al., 2001).”

“The found data is then analyzed, usually using tools available on the web [97,98].”

“The average next generation sequencing experiment generates terabytes of data [Zhang et al., 2011].”

“genome-wide scale in a rapid and cost efficient manner [1,2,3].”

“Recently the next generation DNA sequencing technology has come of age [6].”

“The changing epidemiology of emerging infectious diseases, with more frequent novel outbreaks and faster spread adds to the fact that efficiency in outbreak control and response relies on timely and global access to MGR [1–3].”

“Over the past years, the advent of next-generation DNA sequencing (NGS) shifted the way biologists access and analyze molecular data (Zhang et al. 2011; Goodwin et al. 2016).”