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genome sequence wgs data sets  (Biotechnology Information)

 
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    Biotechnology Information genome sequence wgs data sets
    Clustering of the A. paragallinarum samples based on cgMLST. ( A ) Minimum spanning tree based on the allelic profiles of 1,170 core gene targets from <t>57</t> <t>whole-genome</t> samples using the SeqSphere+ software. ( B ) cgMLST dendrogram displaying 57 whole genome-sequenced A. paragallinarum samples. The distance matrix was built from all pairwise allelic profile comparisons of 1,170 cgMLST targets using the missing values as an own category option in SeqSphere+ software . Samples are color-coded by geographic origin, and dendrograms are rooted by the AP08_SA.
    Genome Sequence Wgs Data Sets, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/wgs+sequencing+data/pmc12977546-91-15-25?v=Biotechnology+Information
    Average 86 stars, based on 1 article reviews
    genome sequence wgs data sets - by Bioz Stars, 2026-07
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    1) Product Images from "A standardized, genome-guided MLST scheme for Avibacterium paragallinarum : enhanced epidemiological typing and validation against existing methods"

    Article Title: A standardized, genome-guided MLST scheme for Avibacterium paragallinarum : enhanced epidemiological typing and validation against existing methods

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/jcm.01267-25

    Clustering of the A. paragallinarum samples based on cgMLST. ( A ) Minimum spanning tree based on the allelic profiles of 1,170 core gene targets from 57 whole-genome samples using the SeqSphere+ software. ( B ) cgMLST dendrogram displaying 57 whole genome-sequenced A. paragallinarum samples. The distance matrix was built from all pairwise allelic profile comparisons of 1,170 cgMLST targets using the missing values as an own category option in SeqSphere+ software . Samples are color-coded by geographic origin, and dendrograms are rooted by the AP08_SA.
    Figure Legend Snippet: Clustering of the A. paragallinarum samples based on cgMLST. ( A ) Minimum spanning tree based on the allelic profiles of 1,170 core gene targets from 57 whole-genome samples using the SeqSphere+ software. ( B ) cgMLST dendrogram displaying 57 whole genome-sequenced A. paragallinarum samples. The distance matrix was built from all pairwise allelic profile comparisons of 1,170 cgMLST targets using the missing values as an own category option in SeqSphere+ software . Samples are color-coded by geographic origin, and dendrograms are rooted by the AP08_SA.

    Techniques Used: Software

    Minimum spanning tree of whole genome-sequenced samples based on two MLST profiles color-coded based on their geographic origin. ( A ) Minimum spanning tree of the WGS samples created using the seven-locus MLST scheme described by Guo et al. . ( B ) Minimum spanning tree of the WGS samples created using the MLST scheme developed in this study.
    Figure Legend Snippet: Minimum spanning tree of whole genome-sequenced samples based on two MLST profiles color-coded based on their geographic origin. ( A ) Minimum spanning tree of the WGS samples created using the seven-locus MLST scheme described by Guo et al. . ( B ) Minimum spanning tree of the WGS samples created using the MLST scheme developed in this study.

    Techniques Used:



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    Clustering of the A. paragallinarum samples based on cgMLST. ( A ) Minimum spanning tree based on the allelic profiles of 1,170 core gene targets from <t>57</t> <t>whole-genome</t> samples using the SeqSphere+ software. ( B ) cgMLST dendrogram displaying 57 whole genome-sequenced A. paragallinarum samples. The distance matrix was built from all pairwise allelic profile comparisons of 1,170 cgMLST targets using the missing values as an own category option in SeqSphere+ software . Samples are color-coded by geographic origin, and dendrograms are rooted by the AP08_SA.
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    Image Search Results


    a) Single nucleotide polymorphisms (SNPs) detected by whole genome sequencing for the three strains when compared to the SC5314 reference genome. b) Overlap between sgRNAs with target binding regions affected by SNPs. The lower left histogram shows the total number of sgRNAs affected for each strain.

    Journal: bioRxiv

    Article Title: Pooled CRISPRi screening reveals fungal-specific vulnerabilities across environments and genetic backgrounds

    doi: 10.64898/2025.12.19.695556

    Figure Lengend Snippet: a) Single nucleotide polymorphisms (SNPs) detected by whole genome sequencing for the three strains when compared to the SC5314 reference genome. b) Overlap between sgRNAs with target binding regions affected by SNPs. The lower left histogram shows the total number of sgRNAs affected for each strain.

    Article Snippet: WGS sequencing data was analyzed using a modified version of the Broad Institute Funpipe workflow with GATK v4.6.1.0 (van der ), Picard v3.1.0 ( Picard: A Set of Command Line Tools (in Java) for Manipulating High-Throughput Sequencing (HTS) Data and Formats such as SAM/BAM/CRAM and VCF , n.d.), bwa199 v0.7.18 , samtools v1.20 , bcftools v1.19 , bedtools v2.31.0 ( ).

    Techniques: Sequencing, Binding Assay

    Summary of clinical correlations adjusted for sex, age of sampling, and stage. A, ChCC ( n = 61) and ( B ) pRCC ( n = 103). CN, copy number; MB, megabase; SNV, single-nucleotide variant; TCRA, T-cell receptor-α; WGII, whole-genome instability index;ll *, P < 0.05.

    Journal: Molecular Cancer Research

    Article Title: Contrasting Features of Papillary and Chromophobe Renal Cell Carcinoma Revealed by Whole-Genome Sequencing

    doi: 10.1158/1541-7786.MCR-25-0616

    Figure Lengend Snippet: Summary of clinical correlations adjusted for sex, age of sampling, and stage. A, ChCC ( n = 61) and ( B ) pRCC ( n = 103). CN, copy number; MB, megabase; SNV, single-nucleotide variant; TCRA, T-cell receptor-α; WGII, whole-genome instability index;ll *, P < 0.05.

    Article Snippet: To address this shortcoming, we report the analysis of whole-genome sequencing (WGS) data generated on tumor–normal (T/N) pairs from 164 patients recruited from NHS Genomic Medicine Centres (GMC) across England, as part of the Genomics England 100,000 Genomes Project (100kGP, RRID: SCR_010502; refs , ).

    Techniques: Sampling, Variant Assay

    Clustering of the A. paragallinarum samples based on cgMLST. ( A ) Minimum spanning tree based on the allelic profiles of 1,170 core gene targets from 57 whole-genome samples using the SeqSphere+ software. ( B ) cgMLST dendrogram displaying 57 whole genome-sequenced A. paragallinarum samples. The distance matrix was built from all pairwise allelic profile comparisons of 1,170 cgMLST targets using the missing values as an own category option in SeqSphere+ software . Samples are color-coded by geographic origin, and dendrograms are rooted by the AP08_SA.

    Journal: Journal of Clinical Microbiology

    Article Title: A standardized, genome-guided MLST scheme for Avibacterium paragallinarum : enhanced epidemiological typing and validation against existing methods

    doi: 10.1128/jcm.01267-25

    Figure Lengend Snippet: Clustering of the A. paragallinarum samples based on cgMLST. ( A ) Minimum spanning tree based on the allelic profiles of 1,170 core gene targets from 57 whole-genome samples using the SeqSphere+ software. ( B ) cgMLST dendrogram displaying 57 whole genome-sequenced A. paragallinarum samples. The distance matrix was built from all pairwise allelic profile comparisons of 1,170 cgMLST targets using the missing values as an own category option in SeqSphere+ software . Samples are color-coded by geographic origin, and dendrograms are rooted by the AP08_SA.

    Article Snippet: A total of 75 A. paragallinarum samples were used in the study, consisting of 45 whole-genome sequence (WGS) data sets from the National Center for Biotechnology Information (NCBI) database in March 2023 and 30 additional samples, including 25 clinical samples (frozen isolates in glycerol, active culture plates, or PCR-positive samples in BHI broth) and five WGS data sets obtained from state diagnostic laboratories, including Salisbury Animal Health Laboratory (SAHL; Salisbury, Maryland); Iowa State Diagnostic Laboratory (Ames, Iowa), Lasher Laboratory (Georgetown, Delaware), Ohio Animal Diseases Diagnostic Laboratory (ADDL; Reynoldsburg, Ohio), and CEVA Animal Health (Lenexa, Kansas).

    Techniques: Software

    Minimum spanning tree of whole genome-sequenced samples based on two MLST profiles color-coded based on their geographic origin. ( A ) Minimum spanning tree of the WGS samples created using the seven-locus MLST scheme described by Guo et al. . ( B ) Minimum spanning tree of the WGS samples created using the MLST scheme developed in this study.

    Journal: Journal of Clinical Microbiology

    Article Title: A standardized, genome-guided MLST scheme for Avibacterium paragallinarum : enhanced epidemiological typing and validation against existing methods

    doi: 10.1128/jcm.01267-25

    Figure Lengend Snippet: Minimum spanning tree of whole genome-sequenced samples based on two MLST profiles color-coded based on their geographic origin. ( A ) Minimum spanning tree of the WGS samples created using the seven-locus MLST scheme described by Guo et al. . ( B ) Minimum spanning tree of the WGS samples created using the MLST scheme developed in this study.

    Article Snippet: A total of 75 A. paragallinarum samples were used in the study, consisting of 45 whole-genome sequence (WGS) data sets from the National Center for Biotechnology Information (NCBI) database in March 2023 and 30 additional samples, including 25 clinical samples (frozen isolates in glycerol, active culture plates, or PCR-positive samples in BHI broth) and five WGS data sets obtained from state diagnostic laboratories, including Salisbury Animal Health Laboratory (SAHL; Salisbury, Maryland); Iowa State Diagnostic Laboratory (Ames, Iowa), Lasher Laboratory (Georgetown, Delaware), Ohio Animal Diseases Diagnostic Laboratory (ADDL; Reynoldsburg, Ohio), and CEVA Animal Health (Lenexa, Kansas).

    Techniques: