GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information.

Museomics is an approach to the DNA sequencing of museum specimens that can generate both biodiversity and sequence information. In this study, we surveyed both the biodiversity information-based database BOLD (Barcode of Life System) and the sequence information database GenBank, by using DNA barcoding data as an example, with the aim of integrating the data from these two databases. DNA barcoding is a method of identifying species from DNA sequences by using short genetic markers. We surveyed how many entries had biodiversity information (such as links to BOLD and specimen IDs) by downloading all fish, insect, and flowering plant data available from the GenBank Nucleotide, and BOLD ID was assigned to 26.2% of entries for insects. In the same way, we downloaded the respective BOLD data and checked the status of links to sequence information. We also investigated how many species do these databases cover, and 7,693 species were found to exist only in BOLD. In the future, as museomics develops as a field, the targeted sequences will be extended not only to DNA barcodes, but also to mitochondrial genomes, other genes, and genome sequences. Consequently, the value of the sequence data will increase. In addition, various species will be sequenced and, thus, biodiversity information such as the evidence specimen photographs used as a basis for species identification, will become even more indispensable. This study contributes to the acceleration of museomics-associated research by using databases in a cross-sectional manner.

NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.

Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank.

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DNA Sequencing Market Size 2024-2028

The DNA sequencing market size is forecast to increase by USD 17.34 billion, at a CAGR of 20.01% between 2023 and 2028.

The market is experiencing significant growth, driven by the increasing adoption of Next-Generation Sequencing (NGS) technologies. NGS offers several advantages over traditional Sanger sequencing, including faster turnaround time, lower costs, and the ability to sequence entire genomes. This technological advancement has led to a surge in demand for DNA sequencing in various applications, including diagnostics, research, and forensics technologies. However, the market faces challenges, most notably the emergence of third-generation sequencing methods. These new technologies, such as PacBio and Oxford Nanopore, offer even faster sequencing speeds and longer read lengths than NGS. As these methods continue to advance, they may disrupt the market dynamics and force companies to innovate or risk becoming obsolete.
Additionally, inadequate resources for DNA sequencing in developing countries pose a significant challenge. Despite the potential benefits of DNA sequencing, many countries lack the necessary infrastructure and financial resources to implement these technologies. Companies that can address these challenges and provide affordable and accessible solutions will be well-positioned to capitalize on the growing demand for DNA sequencing.

What will be the Size of the DNA Sequencing Market during the forecast period?

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The market continues to evolve, driven by advancements in technologies and applications across various sectors. Base calling, a fundamental process in sequencing, is being refined through the use of artificial intelligence and machine learning algorithms. Microbial sequencing, a key application, is revolutionizing fields such as metagenomics and environmental science. Precision medicine, another significant area, is benefiting from the integration of genomic data into clinical workflows, enabling personalized treatment plans. Nanopore sequencing, known for its long read length, is gaining traction in genome assembly and gene expression analysis. Variant calling, a crucial step in identifying genetic mutations, is being enhanced by the integration of multiple data sources and advanced algorithms.

Sample preparation, a critical step in the sequencing process, is being optimized for improved efficiency and cost reduction. Sequencing depth, read length, and sequencing coverage are key performance indicators that continue to evolve, enabling the detection of rare variants and complex genomic structures. Rare disease research is a growing application area, with high-throughput sequencing and exome sequencing playing a pivotal role in identifying disease-causing mutations. Regulatory compliance, data security, and data storage are becoming increasingly important considerations in the market. Cost reduction and workflow optimization are ongoing priorities for sequencing platform providers, with next-generation sequencing (NGS) and Sanger sequencing continuing to coexist in the market.

The ongoing advancements in DNA sequencing technologies and applications are shaping the market dynamics, with genome editing, clinical diagnostics, and forensic science being some of the emerging areas of focus. The integration of cloud computing and library preparation into the sequencing workflow is also transforming the market landscape. In the realm of research, applications such as phylogenetic analysis, methylation analysis, SNP analysis, and quality control are driving the adoption of sequencing technologies. The sequencing error rate, a critical performance metric, is being addressed through the development of advanced algorithms and sequencing reagents. Infectious disease research is another area of significant growth, with NGS playing a crucial role in identifying disease-causing pathogens and understanding their genetic makeup.

Targeted sequencing and CNV analysis are also gaining popularity in this field, enabling the detection of specific genetic variants and chromosomal aberrations. The market is a dynamic and evolving landscape, with ongoing advancements in technologies and applications shaping its future direction. The integration of various components, including base calling, microbial sequencing, precision medicine, variant calling, nanopore sequencing, sample preparation, sequencing depth, read length, rare disease research, sequencing coverage, sequencing reagents, high-throughput sequencing, exome sequencing, regulatory compliance, mutation detection, illumina sequencing, CNV analysis, data storage, library preparation, cost reduction, sequencing platforms, genome editing, clinical diagnostics, next-generation sequencing, Sanger seq

The excel spreadsheet includes sample IDs and labeling information for DNA sequencing raw data. In addition, DNA concentrations for all the biofilm samples analyzed are presented.

This dataset is associated with the following publication: Jeon, Y., l. li, J. Calvillo, H. Ryu, J. Santo Domingo, O. Choi, J. Brown, and Y. Seo. Impact of algal organic matter on the performance, cyanotoxin removal, and biofilms of biologically-active filtration systems. WATER RESEARCH. Elsevier Science Ltd, New York, NY, USA, 184: 116120, (2020).

The tpm metabarcoding DNA sequence database for taxonomic allocations using the Mothur and DADA2 bio-informatic tools

A.C.M. Pozzi1, R. Bouchali1, L. Marjolet1, B. Cournoyer1

1 University of Lyon, UMR Ecologie Microbienne Lyon (LEM), CNRS 5557, INRAE 1418, Université Claude Bernard Lyon 1, VetAgro Sup, Research Team “Bacterial Opportunistic Pathogens and Environment” (BPOE), 69280 Marcy L’Etoile, France.

Corresponding authors:

A.C.M. Pozzi, UMR Microbial Ecology, CNRS 5557, CNRS 1418, VetAgro Sup, Main building, aisle 3, 1st floor, 69280 Marcy-L’Etoile, France. Tel. (+33) 478 87 39 47. Fax. (+33) 472 43 12 23. Email: adrien.meynier_pozzi@vetagro-sup.fr

B. Cournoyer, UMR Microbial Ecology, CNRS 5557, CNRS 1418, VetAgro Sup, Main building, aisle 3, 1st floor, 69280 Marcy-L’Etoile, France. Tel. (+33) 478 87 56 47. Fax. (+33) 472 43 12 23. Email: and benoit.cournoyer@vetagro-sup.fr

Keywords:

BACtpm, Bacteria, tpm, thiopurine-S-methyltransferase EC:2.1.1.67, Nucleotide sequences, PCR products, Next-Generation-Sequencing, OTHU

Description:

The tpm gene codes for the thiopurine-S-methyltransferase (TPMT), an enzyme that can detoxify metalloid-containing oxyanions and xenobiotics (Cournoyer et al., 1998). Bacterial TPMTs radiated apart from human and animal TPMTs, and showed a vertical evolution in line with the 16S rRNA gene molecular phylogeny (Favre‐Bonté et al., 2005).

The tpm database, named BACtpm, was designed to apply the tpm-metabarcoding analytical scheme published in Aigle et al. (2021). It includes the full tpm identifiers, GenBank accession numbers, complete taxonomic records (domain down to strain code) of about 215 nucleotide-long tpm sequences of 840 unique taxa belonging to 139 genera.

Nucleotide sequences of tpm (range: 190-233 nucleotides) were either retrieved from public repositories (GenBank) or made available by B. Cournoyer’s research group. Colin et al. (2020) described the PCR and high throughput Illumina Miseq DNA sequencing procedures used to produce tpm sequences.

BACtpm v.2.0.1 (June 2021 release) is made available under the Creative Commons Attribution 4.0 International Licence. It can be used for the taxonomic allocations of tpm sequences down to the species and strain levels. Data is stored in the csv format enabling future user to reformat it to fit their specific needs.

Acknowledgments:

We thank the worldwide community of microbiologists who made contributions to public databases in the past decades, and made possible the elaboration of the BACtpm database. We also thank the Field Observatory in Urban Hydrology (OTHU, www.graie.org/othu/), Labex IMU (Intelligence des Mondes Urbains), the Greater Lyon Urban Community, the School of Integrated Watershed Sciences H2O'LYON, and the Lyon Urban School for their support in the development of this database. This work was funded by the French national research program for environmental and occupational health of ANSES under the terms of project “Iouqmer” EST 2016/1/120, l'Agence Nationale de la Recherche through ANR-16-CE32-0006, ANR-17-CE04-0010, ANR-17-EURE-0018 and ANR-17-CONV-0004, by the MITI CNRS project named Urbamic, and the French water agency for the Rhône, Mediterranean and Corsica areas through the Desir and DOmic projects. We thank former BPOE lab members who contributed to start and expand the BACtpm database: Céline COLINON, Romain MARTI, Emilie BOURGEOIS, Sébastien RIBUN and Yannick COLIN.

References:

Aigle, A., Colin, Y., Bouchali, R., Bourgeois, E., Marti, R., Ribun, S., Marjolet, L., Pozzi, A.C.M., Misery, B., Colinon, C., Bernardin-Souibgui, C., Wiest, L., Blaha, D., Galia, W., Cournoyer, B., 2021. Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach. Sci. Total Environ. 767, 145425. https://doi.org/10.1016/j.scitotenv.2021.145425

Colin, Y., Bouchali, R., Marjolet, L., Marti, R., Vautrin, F., Voisin, J., Bourgeois, E., Rodriguez-Nava, V., Blaha, D., Winiarski, T., Mermillod-Blondin, F., Cournoyer, B., 2020. Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes. Hydrol. Earth Syst. Sci. 24, 4257–4273. https://doi.org/10.5194/hess-24-4257-2020

Cournoyer, B., Watanabe, S., Vivian, A., 1998. A tellurite-resistance genetic determinant from phytopathogenic pseudomonads encodes a thiopurine methyltransferase: evidence of a widely-conserved family of methyltransferases1The International Collaboration (IC) accession number of the DNA sequence is L49178.1. Biochim. Biophys. Acta BBA - Gene Struct. Expr. 1397, 161–168. https://doi.org/10.1016/S0167-4781(98)00020-7

Favre‐Bonté, S., Ranjard, L., Colinon, C., Prigent‐Combaret, C., Nazaret, S., Cournoyer, B., 2005. Freshwater selenium-methylating bacterial thiopurine methyltransferases: diversity and molecular phylogeny. Environ. Microbiol. 7, 153–164. https://doi.org/10.1111/j.1462-2920.2004.00670.x

COI DNA sequences from select fish in lakes and wadeable streams

The morphology of the first humans in the Americas (Paleoamericans) differs from that of Native Americans, and has raised the question of whether or not there are also differences in origin or genetics. A few populations who survived until relatively recently have been suggested to retain Paleoamerican morphology. One of these populations is from La Jolla. Here, we have generated genome sequence data from four La Jolla individuals in order to investigate these questions

This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

DNA Sequencing Technologies Market Outlook

The global DNA sequencing technologies market size was valued at approximately USD 8.5 billion in 2023 and is projected to grow significantly, reaching around USD 21.4 billion by 2032, reflecting a robust compound annual growth rate (CAGR) of 10.9% during the forecast period. This surge in market size can be attributed to several growth factors, including advances in technology, decreasing costs of sequencing, and the expanding application of sequencing technologies across diverse fields. As demand for personalized medicine and precision agriculture continues to grow, the market is poised for substantial expansion over the next decade.

One of the primary growth factors driving the DNA sequencing technologies market is the continuous advancement in sequencing technologies themselves. The transition from traditional Sanger sequencing to next-generation sequencing (NGS) has revolutionized the field, offering shorter run times, higher throughput, and reduced costs. The advent of third-generation sequencing technologies further amplifies these advantages by providing even longer read lengths, real-time data generation, and more detailed genome assemblies. These technological strides have opened new avenues for research and clinical applications, thereby catalyzing market growth. Additionally, the ongoing miniaturization and automation of sequencing processes have made these technologies more accessible to a wider range of users, further fueling market expansion.

Another significant growth driver is the expanding application of DNA sequencing in clinical diagnostics and personalized medicine. With the increasing prevalence of genetic disorders and cancers, there is a pressing need for precise diagnostic tools that can facilitate early detection and personalized treatment plans. DNA sequencing technologies allow for comprehensive genomic profiling, enabling healthcare providers to tailor therapies based on an individualÂ’s genetic makeup. This personalized approach not only improves treatment outcomes but also minimizes adverse drug reactions, thereby driving the adoption of sequencing technologies in clinical settings. Furthermore, governmental and private investments in genomic research and the establishment of large-scale genomic databases are bolstering the marketÂ’s growth prospects.

The role of DNA Sequencing Instruments in the market is pivotal as they serve as the backbone of sequencing technologies. These instruments have evolved significantly over the years, transitioning from bulky, complex machines to more compact and efficient devices. The advancements in DNA Sequencing Instruments have facilitated the shift towards high-throughput sequencing, enabling researchers to conduct large-scale genomic studies with greater ease and accuracy. This evolution has not only reduced the time and cost associated with sequencing but also expanded its accessibility to a broader range of laboratories and institutions. As the demand for genomic data continues to rise, the development and refinement of these instruments remain crucial to supporting the growing needs of the market.

The agricultural and animal research sectors are also significantly contributing to the growth of the DNA sequencing technologies market. The ability to sequence the genomes of various crops and livestock has profound implications for enhancing food security and sustainability. By identifying genetic markers associated with desirable traits such as drought resistance, pest resistance, and higher yield, researchers can expedite the development of improved plant and animal breeds. This application of DNA sequencing in agriculture not only supports global food supply chains but also aligns with rising environmental and sustainability concerns, thereby providing a robust impetus for market growth.

Regionally, the DNA sequencing technologies market exhibits varying dynamics. North America currently leads the market, driven by the presence of major biotechnology companies, advanced healthcare infrastructure, and substantial investment in genomic research. The regionÂ’s strong focus on personalized medicine and favorable governmental policies further support market growth. Meanwhile, the Asia Pacific region is expected to witness the highest growth rate, with a projected CAGR exceeding 12%. This rapid expansion is attributed to the increasing adoption of sequencing technologies in emerging economies, rising investments in healthcare infrastructure, and growing emphasis on agricultural biotechnology. Europe also plays

Environmental DNA (eDNA) methods complement traditional monitoring and can be configured to detect multiple species simultaneously. One such approach, eDNA metabarcoding, uses high-throughput DNA sequencing to indirectly detect many different organisms, spanning broad taxonomic boundaries, from water samples. We are optimizing a non-invasive, low cost eDNA metabarcoding protocol to be used in conjunction with existing monitoring programs. One resource that is currently lacking for metabarcoding studies in general, including those in the San Francisco Estuary (SFE), is a comprehensive database of DNA barcode reference sequences. Without this foundational data, many species go undetected or misidentified in metabarcoding studies. To meet this need, we generated a custom barcode sequence database for the SFE by DNA sequencing and mining of public DNA seqeunce data for estuarine and freshwater species of interest to monitoring programs and ecological studies. Here we present custom referenc..., Data were collected from two sources. Specimens of fish and invertebrates collected from the San Francisco Estuary were used for Sanger DNA sequencing. DNA extractions were performed using the Qiagen Blood and Tissue kit and PCR was performed using primers to amplify the entire barcode sequence. Raw chromatogram data files were manually examined for quality control, aligned, and flanking and primer sequences were trimmed using CodonCode Aligner. For species without physical specimens, or for those specimens that failed PCR/sequencing/QC, publicly available DNA sequences were downloaded from GenBank, and aligned and trimmed to the barcode region using CodonCode Aligner. The combined experimental and downloaded sequences for each barcode were placed into a single .txt file formatted for use with the DADA2 metabarcoding software. For all sequences, an additional verification step was performed by querying the BLASTn database. A separate metadata file (.csv) was also generated for each barc..., The barcode sequence databases (.txt) files can be opened with any text editor program (e.g., Notepad, TextEdit). The .csv metadata files can be opened with any text editor (e.g., Notepad, TextEdit) or spreadsheet software (e.g., Microsoft Excel).

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Next Generation Sequencing Data Analysis Market Size 2024-2028

The global next generation sequencing data analysis market size is estimated to grow by USD 1.90 billion at a CAGR of 22.58% between 2023 and 2028. The market's growth hinges on several factors, including the escalating demand for personalized medicine, the increasing need for early diagnosis of genetic disorders, and the expanding applications in genomics research. Personalized medicine, tailored to individual genetic makeup, is gaining traction for its targeted and more effective treatment approach. The emphasis on early diagnosis of genetic disorders is driving the demand for advanced genetic testing technologies. Moreover, the broadening applications in genomics research, particularly in understanding genetic mechanisms and disease pathways, are fueling market expansion. These trends collectively highlight the growing significance of genetic testing and personalized medicine in healthcare, underscoring the market's growth trajectory.

What will be the Size of the Next Generation Sequencing Data Analysis Market During the Forecast Period?

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Key Companies & Market Insights

Companies are implementing various strategies, such as strategic alliances, partnerships, mergers and acquisitions, geographical expansion, and product/service launches, to enhance their presence in the market. The report also includes detailed analyses of the competitive landscape of the market and information about key companies, including:

Agilent Technologies Inc., Alphabet Inc., BGI Genomics Co. Ltd., Bio Rad Laboratories Inc., Bionivid Technology Pvt. Ltd., Congenica Ltd., Corewell Health, DNAnexus Inc., DNASTAR Inc., Eurofins Scientific SE, F. Hoffmann La Roche Ltd., Fabric Genomics Inc., Golden Helix Inc., HiberCell Inc., Illumina Inc., Invitae Corp., Macrogen Inc., Oxford Nanopore Technologies plc, Pacific Biosciences of California Inc., Partek Inc., PierianDx Inc., QIAGEN NV, SciGenom Labs Pvt. Ltd., Takara Bio Inc., Thermo Fisher Scientific Inc., and Vela Diagnostics

Qualitative and quantitative analysis of companies has been conducted to help clients understand the wider business environment as well as the strengths and weaknesses of key market players. Data is qualitatively analyzed to categorize companies as pure play, category-focused, industry-focused, and diversified; it is quantitatively analyzed to categorize companies as dominant, leading, strong, tentative, and weak.

Market Segmentation

By End-user

The market share growth by the academic research segment will be significant during the forecast period. The market encompasses DNA sequencing technologies used in genomic science, academic research, and clinical diagnostics. Academic institutions utilize NGS for various applications, such as drug discovery, personalized medicine, and clinical diagnostics.

Get a glance at the market contribution of various segments Download PDF Sample

The academic research segment was valued at USD 221.1 million in 2018. Key drivers include decreasing sequencing costs, user-friendly software, and the demand for precision medicine. NGS enables the analysis of genomic patterns, epigenetics, and biological processes through sequence analysis tools and algorithms. Applications include oncology, genetic research, and tumor genotyping. NGS protocols aid in identifying somatic driver mutations, germline mutations, and resistance mutations. Cancer-related illnesses, financial irregularities, and healthcare professionals benefit from these tools, machine learning techniques, and cloud-based solutions. Additionally, NGS is applied in agriculture, forensics, and genomic studies. Key technologies include Whole-Genome Sequencing, array-based technologies, and clinical. Hence, these factors are expected to drive the market during the forecast period.

By Product

Services play an important role in the market, providing specialized expertise and support to users in analyzing and interpreting their NGS data. The market encompasses various services for Exome Sequencing, Targeted Resequencing, De Novo Sequencing, and Methyl Sequencing. Biotechnology and pharmaceutical companies, along with contract research organizations, utilize these services to analyze and interpret their NGS data. The process involves raw data preprocessing, alignment, variant calling, and annotation, employing advanced tools and algorithms. Service providers ensure accuracy and reliability through quality control measures and optimization of parameters. Technologies like Synthesis (SBS) are integral part. Hence, these factors are expected to drive the growth of the services segment in the market during the forecast period.

Regional Analysis

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North America is estimated to contribute 49% to the growth of the global mark

Statistics of the total DNA sequencing data, the raw cpDNA sequence data extracted from the total DNA sequence data and the processed cpDNA sequence data after trimming (for Illumina reads) or error correction (for Nanopore reads).

This dataset contains single-cell RNA and DNA sequencing data (fastq, n=928) obtained after genome-and-transcriptome separation. The RNA-seq data was obtained by Smart-seq2 amplification and Nextera XT library preparation. The DNA-seq data was obtained either by Gtag library preparation and amplification or by PicoPlex whole-genome amplification followed by Nextera XT library preparation. The single cells originate from a human PDX melanoma model and from HCC38 and HCC38 BL cell lines. The sequencing libraries were sequenced with Illumina instruments.

The global DNA sequencing products market is experiencing robust growth, driven by advancements in sequencing technologies, increasing demand for personalized medicine, and expanding applications in research and diagnostics. The market, estimated at $15 billion in 2025, is projected to exhibit a compound annual growth rate (CAGR) of 15% from 2025 to 2033, reaching an estimated market value of approximately $45 billion by 2033. This significant expansion is fueled by several key factors. Firstly, the decreasing cost of sequencing has made it more accessible to a wider range of users, including research institutions, pharmaceutical companies, and clinical laboratories. Secondly, the rising prevalence of chronic diseases and the increasing focus on preventative healthcare are driving demand for early disease detection and personalized treatment strategies that rely heavily on DNA sequencing data. Thirdly, technological advancements, such as next-generation sequencing (NGS) and single-cell sequencing, are continually improving the speed, accuracy, and affordability of DNA sequencing, further stimulating market growth. The market is segmented by product type (reagents and consumables, equipment) and application (research institutes, commercial entities). Major players like Illumina, Roche, and Thermo Fisher Scientific are at the forefront of innovation, continuously developing new technologies and expanding their market reach. While challenges remain, including data analysis complexities and ethical considerations, the overall market outlook for DNA sequencing products remains exceptionally positive. The geographical distribution of the market reflects the concentration of research and healthcare infrastructure. North America currently holds the largest market share, followed by Europe and Asia Pacific. However, emerging economies in Asia, particularly China and India, are witnessing rapid growth due to increasing investments in healthcare infrastructure and rising adoption of advanced technologies. The competitive landscape is characterized by both established players and emerging companies vying for market share through innovation, strategic partnerships, and acquisitions. Future growth will likely be shaped by the continued development of more accessible and affordable sequencing technologies, integration with artificial intelligence for data analysis, and the expansion of clinical applications of DNA sequencing in diagnostics and therapeutics. This will require ongoing advancements in data management and bioinformatics to effectively handle and interpret the vast quantities of genomic data generated.

Advances in DNA sequencing have made it feasible to gather genomic data for non-model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application were originally developed for other assembly types and we do not know their accuracy for reduced representation libraries. To address this important knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens genomes and compared de novo assemblies by six software programs that are commonly used or promising for this purpose (ABySS, CD-HIT, Stacks, Stacks2, Velvet and VSEARCH). We simulated different mutation rates and types of mutations, and then applied the six assemblers to the simulated datasets, varying assembly parameters. We found substantial variation in software performance across simulations and parameter settings. ABySS failed to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing SNPs, but the addition of insertion and deletion mutations decreased their performance. CD-HIT was the only assembler that consistently recovered a high proportion of true genome fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies from different software programs and the importance of comparing assemblies that result from different parameter settings.

Whole genome sequence data for Bovidae Bos taurus - beef Angus. The data is in "fastq" format.The National Animal Germplasm Program has germplasm for this animal, with the repository number 20545.There are two versions of each file because we did paired end sequencing. There are two reads for each of the 210 data lines (a forward and a reverse read) summing to 420 total. A diagram of this is provided in the Collection Dataset. In the diagram, the two reads would correspond to read 1 and read 3.Resources in this dataset:Resource Title: Animal 20545 Sequence Data - SCINet.File Name: Web Page, url: https://app.globus.org/file-manager?origin_id=904c2108-90cf-11e8-9672-0a6d4e044368&origin_path=/LTS/ADCdatastorage/NAL/published/node32023/tar file containng 14 files. the files are: RAPiD-Genomics_F112_CSU_136201_P001_WA09_i5-515_i7-105_S9_L003_R1_001.fastq.gz RAPiD-Genomics_F112_CSU_136201_P001_WA09_i5-515_i7-105_S9_L003_R2_001.fastq.gz RAPiD-Genomics-F113-CSU-136201-P001-WA09-i5-515-i7-105_S145_L002_R1_001.fastq.gz RAPiD-Genomics-F113-CSU-136201-P001-WA09-i5-515-i7-105_S145_L002_R2_001.fastq.gz RAPiD-Genomics-F113-CSU-136201-P001-WA09-i5-515-i7-105_S9_L001_R1_001.fastq.gz RAPiD-Genomics-F113-CSU-136201-P001-WA09-i5-515-i7-105_S9_L001_R2_001.fastq.gz RAPiD-Genomics-F114-CSU-136201-P001-WA09-i5-515-i7-105_S9_L003_R1_001.fastq.gz RAPiD-Genomics-F114-CSU-136201-P001-WA09-i5-515-i7-105_S9_L003_R2_001.fastq.gz RAPiD-Genomics_F115_CSU_136201_P001_WA09_i5-515_i7-105_S9_L001_R1_001.fastq.gz RAPiD-Genomics_F115_CSU_136201_P001_WA09_i5-515_i7-105_S9_L001_R2_001.fastq.gz RAPiD-Genomics_F115_CSU_136201_P001_WA09_i5-515_i7-105_S9_L002_R1_001.fastq.gz RAPiD-Genomics_F115_CSU_136201_P001_WA09_i5-515_i7-105_S9_L002_R2_001.fastq.gz RAPiD-Genomics_F116_CSU_136201_P001_WA09_i5-515_i7-105_S364_L002_R1_001.fastq.gz RAPiD-Genomics_F116_CSU_136201_P001_WA09_i5-515_i7-105_S364_L002_R2_001.fastq.gzSCINet users: The .tar file can be accessed/retrieved with valid SCINet account at this location: /LTS/ADCdatastorage/NAL/published/node32023/See the SCINet File Transfer guide for more information on moving large files: https://scinet.usda.gov/guides/data/datatransferGlobus users: The files can also be accessed through Globus by following this data link.The user will need to log in to Globus in order to retrieve this data. User accounts are free of charge with several options for signing on. Instructions for creating an account are on the login page.

The deposited data consists of 47 bam files for targeted DNA sequencing and somatic mutation list called by bulk whole-genome sequencing in patients with myelodysplastic syndromes or related myeloid malignancies who received allogeneic stem cell transplantation. The objective of this data collection was to assess whether somatic mutation can be a marker for detecting early relapse. DNA sequencing was performed to identify somatic mutation candidates using samples collected at diagnosis and also performed for the comparison of the sensitivity of detection between digital droplet PCR and next-generation sequencing. We used three different gene panels for targeted DNA sequencing and the gene lists can be found in the cited Blood paper. Read alignment was performed against the GRCh37. In two patients in whom no recurrent driver mutations were identified, whole genome sequencing was performed. After alignment to GRCh37, somatic mutations were called using Genomon2, and identified somatic mutation list was deposited.

The total size of the deposited data is approximately 25 GB (24586652781 bytes).

The global DNA Sequence Analysis Software market is experiencing robust growth, driven by advancements in sequencing technologies, increasing genomic research, and the rising demand for personalized medicine. The market, valued at approximately $2.5 billion in 2025, is projected to exhibit a Compound Annual Growth Rate (CAGR) of 15% from 2025 to 2033. This significant expansion is fueled by several key factors. The decreasing cost of DNA sequencing is making it more accessible for research and clinical applications, leading to a surge in data requiring sophisticated analysis software. Furthermore, the increasing prevalence of chronic diseases and the growing focus on preventative healthcare are boosting the adoption of DNA sequence analysis for diagnostics and treatment planning, particularly within the medical and biological industries. The cloud-based segment is anticipated to witness the highest growth rate due to its scalability, accessibility, and cost-effectiveness compared to on-premises solutions. Major players like Illumina, PacBio, and GenomSys are driving innovation through continuous product development and strategic partnerships, further fueling market expansion. However, the market faces some challenges. Data security and privacy concerns related to sensitive genomic information remain a significant restraint. The complexity of analyzing large datasets requires specialized expertise, potentially limiting adoption in smaller research facilities or clinics. Additionally, the regulatory landscape surrounding genomic data and its use in healthcare varies across different regions, impacting market growth in specific geographical areas. Despite these challenges, the long-term outlook for the DNA Sequence Analysis Software market remains positive, driven by continuous technological advancements, expanding research activities, and growing healthcare investment. The market is expected to reach approximately $7 billion by 2033.

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of information on bacterial phages. It contains multiple phage genomes, which users can BLAST and MegaBLAST, and also hosts a Phage Forum in which users can discuss phage data. Interactive browsing of completed phage genomes is available using the program. The browser allows users to scan the genome for particular features and to download sequence information plus analyses of those features. Views of the genome are generated showing named genes BLAST similarities to other phages predicted tRNAs and other sequence features.