nextseq 500 sequencing platform Illumina Inc Search Results


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  • 93
    Illumina Inc nextseq 500 sequencing platforms
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 Sequencing Platforms, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 1061 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc next generation sequencing
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Next Generation Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 1128 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc nextseq 500 v2 sequencing platform
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 V2 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc illumina sequencing platform
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Illumina Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 694 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina sequencing platform/product/Illumina Inc
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    Illumina Inc nextseq 500 550 v2 sequencing reagent kit
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 550 V2 Sequencing Reagent Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 55 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Illumina Inc nextseq 500 platform rendering 2 × 150 bp pair end sequences
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 Platform Rendering 2 × 150 Bp Pair End Sequences, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc nextseq 500 550 platform
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 550 Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc nextseq 500 platform located
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 Platform Located, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc nextseq 500 platform high output 300 cycle kits
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 Platform High Output 300 Cycle Kits, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 21 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc nextseq 500 mid output
    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina <t>NextSeq</t> 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.
    Nextseq 500 Mid Output, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina NextSeq 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.

    Journal: Environmental Microbiology Reports

    Article Title: Potential KPC‐2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan

    doi: 10.1111/1758-2229.12772

    Figure Lengend Snippet: Schematic circular representation of complete genome sequences of KPC‐2‐producing A. hydrophila GSH8‐2. Short paired‐end whole‐genome sequencing was performed using an Illumina NextSeq 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer). The complete genome sequences of the strains were determined using a PacBio Sequel sequencer for long‐read sequencing [Sequel SMRT Cell 1 M v2 (4/tray]; Sequel sequencing kit v2.1; insert size, approximately 10 kb). De novo assembly was performed using Canu version 1.4 (Koren et al ., 2017 ), minimap version 0.2‐r124 (Li, 2016 ), racon version 1.1.0 (Vaser et al ., 2017 ) and circulator version 1.5.3 (Hunt et al ., 2015 ). Error correction of tentative complete circular sequences was performed using Pilon version 1.18 with Illumina short reads (Walker et al ., 2014 ). Annotation was performed in Prokka version 1.11 (Seemann, 2014 ), InterPro v49.0 (Finn et al ., 2017 ) and NCBI‐BLASTP/BLASTX. Circular representations of complete genomic sequences were visualized using GView server (Petkau et al ., 2010 ). AMR genes were identified by homology searching against the ResFinder database (Zankari et al ., 2012 ). The class 1 integron was assigned in the INTEGRALL database ( http://integrall.bio.ua.pt/ ) (Moura et al ., 2009 ). Visualization of comparative plasmid ORFs organization was performed using Easyfig (Sullivan et al ., 2011 ). For representation of chromosomal DNA, from the inside: slot 1, GC skew; slot 2, GC content; slot 3, ORFs; slot 4, rRNA/tRNA; slots 5–7, BLASTatlas conserved gene analysis indicating three relative strains (see also Supporting Information Fig. S1 ); slot 8, prophage; slot 9, notable ARGs or ARG‐related genes (transposase, ARGs and reductases). In representations of circular plasmids, notable ORFs are highlighted as the indicated colour.

    Article Snippet: These isolates were then subjected to whole‐genome sequencing (WGS) as described previously (Sekizuka et al ., ), using an Illumina NextSeq 500 platform with a 300‐cycle NextSeq 500 Reagent Kit v2 (2 × 150‐mer).

    Techniques: Sequencing, Genomic Sequencing, Plasmid Preparation