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next-generation sequencing data  (Illumina Inc)


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    Illumina Inc next-generation sequencing data
    Next Generation Sequencing Data, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/next+generation+sequencing+data/next+generation+sequencing+data/pm40650042-288-9-8
    Average 90 stars, based on 1 article reviews
    next-generation sequencing data - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Control:

    Article Title: Identifying Mixed Mycobacterium tuberculosis Infection and Laboratory Cross-Contamination during Mycobacterial Sequencing Programs
    Article Snippet: .. 74 As part of the quality control and accreditation of the routine process now operating in these 75 laboratories, we describe an approach to identifying mixed samples using Illumina next generation 76 on S eptem ber 14, 2018 by guest http://jcm .asm .org/ D ow nloaded from sequencing data, illustrating its use by studying over 4,000 consecutive positive cultures from a 77 single reference laboratory. ..

    Sequencing:

    Article Title: Identifying Mixed Mycobacterium tuberculosis Infection and Laboratory Cross-Contamination during Mycobacterial Sequencing Programs
    Article Snippet: .. 74 As part of the quality control and accreditation of the routine process now operating in these 75 laboratories, we describe an approach to identifying mixed samples using Illumina next generation 76 on S eptem ber 14, 2018 by guest http://jcm .asm .org/ D ow nloaded from sequencing data, illustrating its use by studying over 4,000 consecutive positive cultures from a 77 single reference laboratory. ..

    Article Title: High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls
    Article Snippet: .. In addition to noise generated during sequencing, library preparation artefacts represent a major source of errors in Illumina next generation sequencing data [ ], and to help differentiate these sources of error from true biological variation, awareness of other samples data in the same batch enables checks for repeating artefacts that can be batch-specific. ..

    Article Title: High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls.
    Article Snippet: .. In addition to noise generated during sequencing, library preparation artefacts represent a major source of errors in Illumina next generation sequencing data [46], and to help differentiate these sources of error from true biological variation, awareness of other samples data in the same batch enables checks for repeating artefacts that can be batch-specific. ..

    Next-Generation Sequencing:

    Article Title: Multisystem mitochondrial disease caused by a rare m.10038G>A mitochondrial tRNAGly (MT-TG) variant
    Article Snippet: .. Analysis of the next generation sequencing data (Ilumina MiSeq) of the entire mitochondrial genome extracted from the muscle3 revealed a rare m.10038G>A variant (GenBank reference accession number: NC_012920.1) in MTTG (figure B) that was present at variable heteroplasmy levels across tissue types: 15% blood, 40% urinary epithelial cells, and 92% skeletal muscle. ..

    Article Title: Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles
    Article Snippet: .. Illumina next generation sequencing data was generated from swab DNA samples taken on subway stations from Boston, New York, and Sacramento. ..

    Article Title: High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls
    Article Snippet: .. In addition to noise generated during sequencing, library preparation artefacts represent a major source of errors in Illumina next generation sequencing data [ ], and to help differentiate these sources of error from true biological variation, awareness of other samples data in the same batch enables checks for repeating artefacts that can be batch-specific. ..

    Article Title: High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls.
    Article Snippet: .. In addition to noise generated during sequencing, library preparation artefacts represent a major source of errors in Illumina next generation sequencing data [46], and to help differentiate these sources of error from true biological variation, awareness of other samples data in the same batch enables checks for repeating artefacts that can be batch-specific. ..

    Article Title: Secure transmission of genomic data
    Article Snippet: .. For example, with Illumina next generation sequencing data, at least 20 reads covering the SNP would be needed. ..

    Variant Assay:

    Article Title: Multisystem mitochondrial disease caused by a rare m.10038G>A mitochondrial tRNAGly (MT-TG) variant
    Article Snippet: .. Analysis of the next generation sequencing data (Ilumina MiSeq) of the entire mitochondrial genome extracted from the muscle3 revealed a rare m.10038G>A variant (GenBank reference accession number: NC_012920.1) in MTTG (figure B) that was present at variable heteroplasmy levels across tissue types: 15% blood, 40% urinary epithelial cells, and 92% skeletal muscle. ..

    other:

    Article Title: Episodic weakness and axonal sensorimotor neuropathy caused by a mitochondrial MT-ATP6 mutation.
    Article Snippet: Analysis of the next generation sequencing (NGS) data (MiSeq, Ilumina, San Diego, CA) of the entire mitochondrial genome extracted from the blood revealed a homoplasmic m.9185T > C variant (NC_012920) in MT-ATP6 (Fig. 1B).

    Article Title: Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.).
    Article Snippet: NGS-QCbox and Raspberry for parallel, automated and rapid quality control analysis of large-scale next generation sequencing (Illumina) data.

    Generated:

    Article Title: Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles
    Article Snippet: .. Illumina next generation sequencing data was generated from swab DNA samples taken on subway stations from Boston, New York, and Sacramento. ..

    Article Title: High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls
    Article Snippet: .. In addition to noise generated during sequencing, library preparation artefacts represent a major source of errors in Illumina next generation sequencing data [ ], and to help differentiate these sources of error from true biological variation, awareness of other samples data in the same batch enables checks for repeating artefacts that can be batch-specific. ..

    Article Title: High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls.
    Article Snippet: .. In addition to noise generated during sequencing, library preparation artefacts represent a major source of errors in Illumina next generation sequencing data [46], and to help differentiate these sources of error from true biological variation, awareness of other samples data in the same batch enables checks for repeating artefacts that can be batch-specific. ..



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    Data preprocessing workflow. When analyzing NGS datasets with KPop, one can optionally pre-process sequencing reads in order to eliminate biases and/or have the method focus on specific parts of the genome. For instance, one might align reads to a (pan-)genome and separate them into reads that align (likely to originate from the organism being studied) and reads that do not (likely to come from contaminations). Furthermore, reads that do map to the pan-genome might be separated into groups specific to different genomic features; for instance, one might align them to a set of MLST genes or AMR genes. Full k -mer spectra would then be separately obtained from each group of reads (contaminations, pan-genomic, MLST genes, AMR genes) and given as input to downstream/classification methods. The choice of the group of reads from which spectra are computed determines the set of sequences seen by the method, and hence the scope of the classification

    Journal: Genome Biology

    Article Title: KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings

    doi: 10.1186/s13059-025-03585-8

    Figure Lengend Snippet: Data preprocessing workflow. When analyzing NGS datasets with KPop, one can optionally pre-process sequencing reads in order to eliminate biases and/or have the method focus on specific parts of the genome. For instance, one might align reads to a (pan-)genome and separate them into reads that align (likely to originate from the organism being studied) and reads that do not (likely to come from contaminations). Furthermore, reads that do map to the pan-genome might be separated into groups specific to different genomic features; for instance, one might align them to a set of MLST genes or AMR genes. Full k -mer spectra would then be separately obtained from each group of reads (contaminations, pan-genomic, MLST genes, AMR genes) and given as input to downstream/classification methods. The choice of the group of reads from which spectra are computed determines the set of sequences seen by the method, and hence the scope of the classification

    Article Snippet: In order to do so, simulated next-generation sequencing (NGS) data was generated for each genome using ART [ ], emulating Illumina HiSeq 2500 paired-end reads of length 150 bp with an average coverage of 20-fold.

    Techniques: Sequencing