chikv puerto rico strain 2014 Search Results


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  • 88
    Oxford Nanopore high titer chikungunya virus
    High Titer Chikungunya Virus, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/high titer chikungunya virus/product/Oxford Nanopore
    Average 88 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
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    99
    Illumina Inc illumina miseq platform
    MetaPORE analysis of <t>Illumina</t> <t>MiSeq</t> data from samples containing CHIKV and EBOV. Taxonomic donut charts were generated from Illumina MiSeq data corresponding to the Chik1 run ( a ) and Ebola1 run ( b ) using the MetaPORE bioinformatics analysis pipeline. The total number of MiSeq reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of reads (n = 100,000) was analyzed using MetaPORE. Coverage and pairwise identity plots were generated from MiSeq CHIKV reads from the Chik1 sample (248,677 of 3,235,099 reads, 7.7 %) ( c ), or EBOV reads from the Ebola1 sample (20,820 of 2,743,589 reads, 0.76 %) ( d ), identified using SURPI analysis and LASTZ mapping {Harris, 2007 #34} at an e-value of 10-5 to the closest matching reference genome. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the June 2014 and January 2015 NT databases as the reference databases for the CHIKV and EBOV samples, respectively.
    Illumina Miseq Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 41500 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina miseq platform/product/Illumina Inc
    Average 99 stars, based on 41500 article reviews
    Price from $9.99 to $1999.99
    illumina miseq platform - by Bioz Stars, 2020-07
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    89
    Thermo Fisher pcr ii topo ta vector
    MetaPORE analysis of <t>Illumina</t> <t>MiSeq</t> data from samples containing CHIKV and EBOV. Taxonomic donut charts were generated from Illumina MiSeq data corresponding to the Chik1 run ( a ) and Ebola1 run ( b ) using the MetaPORE bioinformatics analysis pipeline. The total number of MiSeq reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of reads (n = 100,000) was analyzed using MetaPORE. Coverage and pairwise identity plots were generated from MiSeq CHIKV reads from the Chik1 sample (248,677 of 3,235,099 reads, 7.7 %) ( c ), or EBOV reads from the Ebola1 sample (20,820 of 2,743,589 reads, 0.76 %) ( d ), identified using SURPI analysis and LASTZ mapping {Harris, 2007 #34} at an e-value of 10-5 to the closest matching reference genome. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the June 2014 and January 2015 NT databases as the reference databases for the CHIKV and EBOV samples, respectively.
    Pcr Ii Topo Ta Vector, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 108 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr ii topo ta vector/product/Thermo Fisher
    Average 89 stars, based on 108 article reviews
    Price from $9.99 to $1999.99
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    Lucigen Corp ampliscribe t7 flash transcription kit
    MetaPORE analysis of <t>Illumina</t> <t>MiSeq</t> data from samples containing CHIKV and EBOV. Taxonomic donut charts were generated from Illumina MiSeq data corresponding to the Chik1 run ( a ) and Ebola1 run ( b ) using the MetaPORE bioinformatics analysis pipeline. The total number of MiSeq reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of reads (n = 100,000) was analyzed using MetaPORE. Coverage and pairwise identity plots were generated from MiSeq CHIKV reads from the Chik1 sample (248,677 of 3,235,099 reads, 7.7 %) ( c ), or EBOV reads from the Ebola1 sample (20,820 of 2,743,589 reads, 0.76 %) ( d ), identified using SURPI analysis and LASTZ mapping {Harris, 2007 #34} at an e-value of 10-5 to the closest matching reference genome. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the June 2014 and January 2015 NT databases as the reference databases for the CHIKV and EBOV samples, respectively.
    Ampliscribe T7 Flash Transcription Kit, supplied by Lucigen Corp, used in various techniques. Bioz Stars score: 92/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ampliscribe t7 flash transcription kit/product/Lucigen Corp
    Average 92 stars, based on 18 article reviews
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    Corning Life Sciences normal human serum
    MetaPORE analysis of <t>Illumina</t> <t>MiSeq</t> data from samples containing CHIKV and EBOV. Taxonomic donut charts were generated from Illumina MiSeq data corresponding to the Chik1 run ( a ) and Ebola1 run ( b ) using the MetaPORE bioinformatics analysis pipeline. The total number of MiSeq reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of reads (n = 100,000) was analyzed using MetaPORE. Coverage and pairwise identity plots were generated from MiSeq CHIKV reads from the Chik1 sample (248,677 of 3,235,099 reads, 7.7 %) ( c ), or EBOV reads from the Ebola1 sample (20,820 of 2,743,589 reads, 0.76 %) ( d ), identified using SURPI analysis and LASTZ mapping {Harris, 2007 #34} at an e-value of 10-5 to the closest matching reference genome. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the June 2014 and January 2015 NT databases as the reference databases for the CHIKV and EBOV samples, respectively.
    Normal Human Serum, supplied by Corning Life Sciences, used in various techniques. Bioz Stars score: 92/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/normal human serum/product/Corning Life Sciences
    Average 92 stars, based on 3 article reviews
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    Image Search Results


    MetaPORE analysis of Illumina MiSeq data from samples containing CHIKV and EBOV. Taxonomic donut charts were generated from Illumina MiSeq data corresponding to the Chik1 run ( a ) and Ebola1 run ( b ) using the MetaPORE bioinformatics analysis pipeline. The total number of MiSeq reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of reads (n = 100,000) was analyzed using MetaPORE. Coverage and pairwise identity plots were generated from MiSeq CHIKV reads from the Chik1 sample (248,677 of 3,235,099 reads, 7.7 %) ( c ), or EBOV reads from the Ebola1 sample (20,820 of 2,743,589 reads, 0.76 %) ( d ), identified using SURPI analysis and LASTZ mapping {Harris, 2007 #34} at an e-value of 10-5 to the closest matching reference genome. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the June 2014 and January 2015 NT databases as the reference databases for the CHIKV and EBOV samples, respectively.

    Journal: Genome Medicine

    Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

    doi: 10.1186/s13073-015-0220-9

    Figure Lengend Snippet: MetaPORE analysis of Illumina MiSeq data from samples containing CHIKV and EBOV. Taxonomic donut charts were generated from Illumina MiSeq data corresponding to the Chik1 run ( a ) and Ebola1 run ( b ) using the MetaPORE bioinformatics analysis pipeline. The total number of MiSeq reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of reads (n = 100,000) was analyzed using MetaPORE. Coverage and pairwise identity plots were generated from MiSeq CHIKV reads from the Chik1 sample (248,677 of 3,235,099 reads, 7.7 %) ( c ), or EBOV reads from the Ebola1 sample (20,820 of 2,743,589 reads, 0.76 %) ( d ), identified using SURPI analysis and LASTZ mapping {Harris, 2007 #34} at an e-value of 10-5 to the closest matching reference genome. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the June 2014 and January 2015 NT databases as the reference databases for the CHIKV and EBOV samples, respectively.

    Article Snippet: Example 1: Nanopore sequencing of high-titer chikungunya virus (Flow cell #1) To test the ability of nanopore sequencing to identify metagenomic reads from a clinical sample, we first analyzed a plasma sample harboring high-titer CHIKV and previously sequenced on an Illumina MiSeq platform (Fig. ) [ ].

    Techniques: Generated

    Metagenomic sequencing workflow for MinION nanopore sequencing compared to Illumina MiSeq sequencing. a Overall workflow. b Steps in the MetaPORE real-time analysis pipeline. The turnaround time for sample-to-detection nanopore sequencing, defined here as the cumulative time taken for nucleic acid extraction, reverse transcription, library preparation, sequencing, MetaPORE bioinformatics analysis, and pathogen detection, was under 6 hr, while Illumina sequencing took over 20 hr. The time differential is accounted for by increased times for library quantitation, sequencing, and bioinformatics analysis with the Illumina protocol. *Assumes a 12-hr 50-bp single-end MiSeq run of ~12–15 million reads, with 50 bp the minimum estimated read length needed for accurate pathogen identification. **Denotes estimated average SURPI bioinformatics analysis run length for MiSeq data [ 19 ]. The stopwatch is depicted as a 12-hr clock

    Journal: Genome Medicine

    Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

    doi: 10.1186/s13073-015-0220-9

    Figure Lengend Snippet: Metagenomic sequencing workflow for MinION nanopore sequencing compared to Illumina MiSeq sequencing. a Overall workflow. b Steps in the MetaPORE real-time analysis pipeline. The turnaround time for sample-to-detection nanopore sequencing, defined here as the cumulative time taken for nucleic acid extraction, reverse transcription, library preparation, sequencing, MetaPORE bioinformatics analysis, and pathogen detection, was under 6 hr, while Illumina sequencing took over 20 hr. The time differential is accounted for by increased times for library quantitation, sequencing, and bioinformatics analysis with the Illumina protocol. *Assumes a 12-hr 50-bp single-end MiSeq run of ~12–15 million reads, with 50 bp the minimum estimated read length needed for accurate pathogen identification. **Denotes estimated average SURPI bioinformatics analysis run length for MiSeq data [ 19 ]. The stopwatch is depicted as a 12-hr clock

    Article Snippet: Example 1: Nanopore sequencing of high-titer chikungunya virus (Flow cell #1) To test the ability of nanopore sequencing to identify metagenomic reads from a clinical sample, we first analyzed a plasma sample harboring high-titer CHIKV and previously sequenced on an Illumina MiSeq platform (Fig. ) [ ].

    Techniques: Sequencing, Nanopore Sequencing, Quantitation Assay

    Metagenomic identification of EBOV from a clinical blood sample by nanopore sequencing and MetaPORE real-time bioinformatics analysis. Nanopore data generated from the Ebola2 library and sequenced on flow cell #3 were analyzed in real time using the MetaPORE bioinformatics analysis pipeline, and compared to corresponding Illumina MiSeq data. a Time line of nanopore sequencing runs on flow cell #3 with sample reloading, plotted as a function of elapsed time in hours since the start of flow cell sequencing. b Cumulative numbers of all sequenced reads (black line) and target viral reads (red line) from the nanopore run (left panel) or MiSeq run (right panel), plotted as a function of individual sequencing run time in minutes. c Taxonomic donut charts generated by real-time MetaPORE analysis of the nanopore reads (left panel) and post-run analysis of the MiSeq reads (right panel). The total number of reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of MiSeq reads (n = 100,000) was analyzed using MetaPORE. d Coverage and pairwise identity plots generated from nanopore (left panel) or MiSeq data (right panel) by mapping reads aligning to EBOV to the closest matching reference genome ((e), asterisk). e Whole-genome phylogeny of EBOV. Representative EBOV genome sequences, including those from the 2014-2015 West Africa outbreak (tan) and 2014 DRC outbreak (pink), are included. Branch lengths are drawn proportionally to the number of nucleotide substitutions per position, and support values are shown for each node. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the January 2015 NT reference database.

    Journal: Genome Medicine

    Article Title: Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

    doi: 10.1186/s13073-015-0220-9

    Figure Lengend Snippet: Metagenomic identification of EBOV from a clinical blood sample by nanopore sequencing and MetaPORE real-time bioinformatics analysis. Nanopore data generated from the Ebola2 library and sequenced on flow cell #3 were analyzed in real time using the MetaPORE bioinformatics analysis pipeline, and compared to corresponding Illumina MiSeq data. a Time line of nanopore sequencing runs on flow cell #3 with sample reloading, plotted as a function of elapsed time in hours since the start of flow cell sequencing. b Cumulative numbers of all sequenced reads (black line) and target viral reads (red line) from the nanopore run (left panel) or MiSeq run (right panel), plotted as a function of individual sequencing run time in minutes. c Taxonomic donut charts generated by real-time MetaPORE analysis of the nanopore reads (left panel) and post-run analysis of the MiSeq reads (right panel). The total number of reads analyzed is shown in the center of the donut. Note that given computational time constraints, only a subset of MiSeq reads (n = 100,000) was analyzed using MetaPORE. d Coverage and pairwise identity plots generated from nanopore (left panel) or MiSeq data (right panel) by mapping reads aligning to EBOV to the closest matching reference genome ((e), asterisk). e Whole-genome phylogeny of EBOV. Representative EBOV genome sequences, including those from the 2014-2015 West Africa outbreak (tan) and 2014 DRC outbreak (pink), are included. Branch lengths are drawn proportionally to the number of nucleotide substitutions per position, and support values are shown for each node. Data were analyzed in MetaPORE on a 64-core Ubuntu Linux server using the January 2015 NT reference database.

    Article Snippet: Example 1: Nanopore sequencing of high-titer chikungunya virus (Flow cell #1) To test the ability of nanopore sequencing to identify metagenomic reads from a clinical sample, we first analyzed a plasma sample harboring high-titer CHIKV and previously sequenced on an Illumina MiSeq platform (Fig. ) [ ].

    Techniques: Nanopore Sequencing, Generated, Flow Cytometry, Sequencing