long amplicon Search Results


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  • 90
    Roche long amplicon pipeline 1
    Long Amplicon Pipeline 1, supplied by Roche, used in various techniques. Bioz Stars score: 90/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon pipeline 1/product/Roche
    Average 90 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    long amplicon pipeline 1 - by Bioz Stars, 2020-08
    90/100 stars
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    92
    Pacific Biosciences long amplicon analysis module
    Sequence alignment highlighting a recurring insertion error in some bootstrap samples. The alignment corresponds to the consensus sequence for a part of the <t>amplicon</t> from a locus_6_7045710_7052049 (Query) and b locus_1_25390617_25396540 (Query) on maize chromosome 6 and 1 respectively compared to the B73 v3 reference sequence (Sbjct)
    Long Amplicon Analysis Module, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon analysis module/product/Pacific Biosciences
    Average 92 stars, based on 20 article reviews
    Price from $9.99 to $1999.99
    long amplicon analysis module - by Bioz Stars, 2020-08
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    93
    Illumina Inc long amplicons
    Sequence alignment highlighting a recurring insertion error in some bootstrap samples. The alignment corresponds to the consensus sequence for a part of the <t>amplicon</t> from a locus_6_7045710_7052049 (Query) and b locus_1_25390617_25396540 (Query) on maize chromosome 6 and 1 respectively compared to the B73 v3 reference sequence (Sbjct)
    Long Amplicons, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicons/product/Illumina Inc
    Average 93 stars, based on 16 article reviews
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    long amplicons - by Bioz Stars, 2020-08
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    84
    TaKaRa long amplicon taq
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Amplicon Taq, supplied by TaKaRa, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon taq/product/TaKaRa
    Average 84 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    long amplicon taq - by Bioz Stars, 2020-08
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    93
    Pacific Biosciences pacbio long amplicons
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Pacbio Long Amplicons, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pacbio long amplicons/product/Pacific Biosciences
    Average 93 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    pacbio long amplicons - by Bioz Stars, 2020-08
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    99
    TaKaRa long amplicon taq polymerase
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Amplicon Taq Polymerase, supplied by TaKaRa, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon taq polymerase/product/TaKaRa
    Average 99 stars, based on 6 article reviews
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    long amplicon taq polymerase - by Bioz Stars, 2020-08
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    93
    Pacific Biosciences long amplicon analysis laa
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Amplicon Analysis Laa, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon analysis laa/product/Pacific Biosciences
    Average 93 stars, based on 7 article reviews
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    long amplicon analysis laa - by Bioz Stars, 2020-08
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    85
    Thermo Fisher long pcr amplicon
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Pcr Amplicon, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long pcr amplicon/product/Thermo Fisher
    Average 85 stars, based on 9 article reviews
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    long pcr amplicon - by Bioz Stars, 2020-08
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    93
    Oxford Nanopore nanopore long amplicon
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Nanopore Long Amplicon, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nanopore long amplicon/product/Oxford Nanopore
    Average 93 stars, based on 3 article reviews
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    nanopore long amplicon - by Bioz Stars, 2020-08
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    90
    Pacific Biosciences long amplicon analysis protocol
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Amplicon Analysis Protocol, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon analysis protocol/product/Pacific Biosciences
    Average 90 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    long amplicon analysis protocol - by Bioz Stars, 2020-08
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    92
    Pacific Biosciences long amplicon sequencing
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Amplicon Sequencing, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon sequencing/product/Pacific Biosciences
    Average 92 stars, based on 12 article reviews
    Price from $9.99 to $1999.99
    long amplicon sequencing - by Bioz Stars, 2020-08
    92/100 stars
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    88
    Pacific Biosciences long amplicon analysis tool
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Amplicon Analysis Tool, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 88/100, based on 56 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon analysis tool/product/Pacific Biosciences
    Average 88 stars, based on 56 article reviews
    Price from $9.99 to $1999.99
    long amplicon analysis tool - by Bioz Stars, 2020-08
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    92
    Thermo Fisher 112 nucleotide long amplicon
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    112 Nucleotide Long Amplicon, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/112 nucleotide long amplicon/product/Thermo Fisher
    Average 92 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    112 nucleotide long amplicon - by Bioz Stars, 2020-08
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    92
    Thermo Fisher 400 bp long amplicons
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    400 Bp Long Amplicons, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/400 bp long amplicons/product/Thermo Fisher
    Average 92 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    400 bp long amplicons - by Bioz Stars, 2020-08
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    88
    Pacific Biosciences long range pcr amplicons
    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long <t>amplicon</t> DNA polymerase (Sigma-Aldrich <t>Taq</t> vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.
    Long Range Pcr Amplicons, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 88/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long range pcr amplicons/product/Pacific Biosciences
    Average 88 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    long range pcr amplicons - by Bioz Stars, 2020-08
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    86
    Thermo Fisher preparing long amplicon libraries
    mtDNA sequencing coverage per sample. This graph represents a polar plot, the coverage (log 10 scale) for each 100-bp mitochondrial genome window for each of the samples, and the grey highlighted areas in the graph represent the <t>amplicon</t> overlap.
    Preparing Long Amplicon Libraries, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/preparing long amplicon libraries/product/Thermo Fisher
    Average 86 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    preparing long amplicon libraries - by Bioz Stars, 2020-08
    86/100 stars
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    91
    Oxford Nanopore sequencing long amplicon sequencing
    Graphical presentation of the data analysis pipeline. 2D raw reads (1) were size-selected (minimum read length of 6.5 kb) (2) and mapped against the three reference genomes, in order to assign the reads by species and genomic target (3). Only those reads that matched our quality filters (similarity fraction: 0.6 [0.5 for adAmp3, 6 and 7], length fraction: 0.7 [0.5 for adAmp3, 6 and 7]) were included in further analyses (4). Per <t>amplicon</t> sixteen reads (minimum number of reads that mapped to an amplicon—amAmp6) were selected and aligned to each other independent of a reference sequence to build the nanopore-derived consensus sequence (5). Finally, the consensus sequence and the reference sequence were aligned (6). In order to correct the genomic reference sequences of the mrjp gene cluster of A. mellifera , A. florea and A. dorsata , assembly gaps (N) and local mis-assemblies were identified based on this consensus/reference sequence alignment. Assembly gaps (N) in the reference sequence were replaced with the consensus sequence and mis-assemblies were either discarded (when only present in the reference but not in the consensus sequence) or included (when only present in the consensus but not in the reference sequence).
    Sequencing Long Amplicon Sequencing, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/sequencing long amplicon sequencing/product/Oxford Nanopore
    Average 91 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    sequencing long amplicon sequencing - by Bioz Stars, 2020-08
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    93
    Oxford Nanopore long amplicon nanopore protocol
    Graphical presentation of the data analysis pipeline. 2D raw reads (1) were size-selected (minimum read length of 6.5 kb) (2) and mapped against the three reference genomes, in order to assign the reads by species and genomic target (3). Only those reads that matched our quality filters (similarity fraction: 0.6 [0.5 for adAmp3, 6 and 7], length fraction: 0.7 [0.5 for adAmp3, 6 and 7]) were included in further analyses (4). Per <t>amplicon</t> sixteen reads (minimum number of reads that mapped to an amplicon—amAmp6) were selected and aligned to each other independent of a reference sequence to build the nanopore-derived consensus sequence (5). Finally, the consensus sequence and the reference sequence were aligned (6). In order to correct the genomic reference sequences of the mrjp gene cluster of A. mellifera , A. florea and A. dorsata , assembly gaps (N) and local mis-assemblies were identified based on this consensus/reference sequence alignment. Assembly gaps (N) in the reference sequence were replaced with the consensus sequence and mis-assemblies were either discarded (when only present in the reference but not in the consensus sequence) or included (when only present in the consensus but not in the reference sequence).
    Long Amplicon Nanopore Protocol, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 93/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/long amplicon nanopore protocol/product/Oxford Nanopore
    Average 93 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    long amplicon nanopore protocol - by Bioz Stars, 2020-08
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    Image Search Results


    Sequence alignment highlighting a recurring insertion error in some bootstrap samples. The alignment corresponds to the consensus sequence for a part of the amplicon from a locus_6_7045710_7052049 (Query) and b locus_1_25390617_25396540 (Query) on maize chromosome 6 and 1 respectively compared to the B73 v3 reference sequence (Sbjct)

    Journal: BMC Bioinformatics

    Article Title: Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries

    doi: 10.1186/s12859-018-2293-0

    Figure Lengend Snippet: Sequence alignment highlighting a recurring insertion error in some bootstrap samples. The alignment corresponds to the consensus sequence for a part of the amplicon from a locus_6_7045710_7052049 (Query) and b locus_1_25390617_25396540 (Query) on maize chromosome 6 and 1 respectively compared to the B73 v3 reference sequence (Sbjct)

    Article Snippet: In contrast, despite read depths in excess of 100X per amplicon, the standard long amplicon analysis module from Pacific Biosciences generated unexpected numbers of amplicon sequences with substantial inaccuracies in the consensus sequences.

    Techniques: Sequencing, Amplification

    Graphical representation of the C3S-LAA process and pipeline. a Raw reads comprised of multiple subreads are depicted for three different amplicons [green, fuchsia and blue boxes; different shades of color are used to portray variable subread sequence qualities (darker shading portrays higher quality)]. Subreads are separated by a shared adapter sequence (grey boxes). The higher quality CCS read for each raw read is used to cluster the corresponding raw reads into CCS-based cluster groups. Error correction is performed per CCS-based cluster, producing top quality consequences sequences, followed by assembly of any overlapping consensus sequences. b A single run parameters file is used by all components of the pipeline. The grey highlighted rectangles represent two main steps of C3S-LAA. (i) Using the CCS reads generated by the SMRT analysis reads of insert protocol, C3S clusters the raw reads according to each barcode-primer pair combination, producing files of read identifiers to whitelist the corresponding raw reads. (ii) Raw read clusters are passed to Quiver to generate amplicon-specific consensus sequences, which are then passed to Minimus for sequence assembly. Rectangles with folded corners represent single files or multiple files (depicted as stacks of files) and those with rounded edges represent scripts and tools. Arrows indicates output files that are generated. Connecting lines with dots at one end depict input files, with the dot corresponding to the source data for the connected script or tool

    Journal: BMC Bioinformatics

    Article Title: Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries

    doi: 10.1186/s12859-018-2293-0

    Figure Lengend Snippet: Graphical representation of the C3S-LAA process and pipeline. a Raw reads comprised of multiple subreads are depicted for three different amplicons [green, fuchsia and blue boxes; different shades of color are used to portray variable subread sequence qualities (darker shading portrays higher quality)]. Subreads are separated by a shared adapter sequence (grey boxes). The higher quality CCS read for each raw read is used to cluster the corresponding raw reads into CCS-based cluster groups. Error correction is performed per CCS-based cluster, producing top quality consequences sequences, followed by assembly of any overlapping consensus sequences. b A single run parameters file is used by all components of the pipeline. The grey highlighted rectangles represent two main steps of C3S-LAA. (i) Using the CCS reads generated by the SMRT analysis reads of insert protocol, C3S clusters the raw reads according to each barcode-primer pair combination, producing files of read identifiers to whitelist the corresponding raw reads. (ii) Raw read clusters are passed to Quiver to generate amplicon-specific consensus sequences, which are then passed to Minimus for sequence assembly. Rectangles with folded corners represent single files or multiple files (depicted as stacks of files) and those with rounded edges represent scripts and tools. Arrows indicates output files that are generated. Connecting lines with dots at one end depict input files, with the dot corresponding to the source data for the connected script or tool

    Article Snippet: In contrast, despite read depths in excess of 100X per amplicon, the standard long amplicon analysis module from Pacific Biosciences generated unexpected numbers of amplicon sequences with substantial inaccuracies in the consensus sequences.

    Techniques: Sequencing, Generated, Amplification

    Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long amplicon DNA polymerase (Sigma-Aldrich Taq vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.

    Journal: bioRxiv

    Article Title: Full-coverage sequencing of HIV-1 provirus from a reference plasmid

    doi: 10.1101/611848

    Figure Lengend Snippet: Assembled HXB2 plasmid, varying base caller and polymerase. Each pane (n=6) summarizes the results of contig curation. Tan boxes contain alignments of reference/blastn hits to contig (Black line). Divergence from reference decreases with newer base callers, and with long amplicon DNA polymerase (Sigma-Aldrich Taq vs. LA Taq by Takara). Annotations below the black lines were automatically imported with SnapGene and represent sequences with minimal/no divergence from common cloning features. The regions corresponding to HXB2 are between red boxes (LTRs). Viewed in SnapGene.

    Article Snippet: Two independent experiments (PCR-barcoded libraries made with Takara Long Amplicon Taq and Sigma-Aldrich Taq master mixes) yielded at least 20 single nucleotide variants which differed from the reference sequence.

    Techniques: Plasmid Preparation, Amplification, Clone Assay

    mtDNA sequencing coverage per sample. This graph represents a polar plot, the coverage (log 10 scale) for each 100-bp mitochondrial genome window for each of the samples, and the grey highlighted areas in the graph represent the amplicon overlap.

    Journal: Bioinformatics and Biology Insights

    Article Title: A Protocol for mtGenome Analysis on Large Sample Numbers

    doi: 10.4137/BBI.S14623

    Figure Lengend Snippet: mtDNA sequencing coverage per sample. This graph represents a polar plot, the coverage (log 10 scale) for each 100-bp mitochondrial genome window for each of the samples, and the grey highlighted areas in the graph represent the amplicon overlap.

    Article Snippet: ION PGM™ barcode library construction The barcode library construction was performed following the protocol “Preparing Long Amplicon Libraries” (Life Technologies) and using the Ion Xpress™ Plus Fragment Library Kit (Life Technologies).

    Techniques: Sequencing, Amplification

    Graphical presentation of the data analysis pipeline. 2D raw reads (1) were size-selected (minimum read length of 6.5 kb) (2) and mapped against the three reference genomes, in order to assign the reads by species and genomic target (3). Only those reads that matched our quality filters (similarity fraction: 0.6 [0.5 for adAmp3, 6 and 7], length fraction: 0.7 [0.5 for adAmp3, 6 and 7]) were included in further analyses (4). Per amplicon sixteen reads (minimum number of reads that mapped to an amplicon—amAmp6) were selected and aligned to each other independent of a reference sequence to build the nanopore-derived consensus sequence (5). Finally, the consensus sequence and the reference sequence were aligned (6). In order to correct the genomic reference sequences of the mrjp gene cluster of A. mellifera , A. florea and A. dorsata , assembly gaps (N) and local mis-assemblies were identified based on this consensus/reference sequence alignment. Assembly gaps (N) in the reference sequence were replaced with the consensus sequence and mis-assemblies were either discarded (when only present in the reference but not in the consensus sequence) or included (when only present in the consensus but not in the reference sequence).

    Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

    Article Title: Comparative analyses of the major royal jelly protein gene cluster in three Apis species with long amplicon sequencing

    doi: 10.1093/dnares/dsw064

    Figure Lengend Snippet: Graphical presentation of the data analysis pipeline. 2D raw reads (1) were size-selected (minimum read length of 6.5 kb) (2) and mapped against the three reference genomes, in order to assign the reads by species and genomic target (3). Only those reads that matched our quality filters (similarity fraction: 0.6 [0.5 for adAmp3, 6 and 7], length fraction: 0.7 [0.5 for adAmp3, 6 and 7]) were included in further analyses (4). Per amplicon sixteen reads (minimum number of reads that mapped to an amplicon—amAmp6) were selected and aligned to each other independent of a reference sequence to build the nanopore-derived consensus sequence (5). Finally, the consensus sequence and the reference sequence were aligned (6). In order to correct the genomic reference sequences of the mrjp gene cluster of A. mellifera , A. florea and A. dorsata , assembly gaps (N) and local mis-assemblies were identified based on this consensus/reference sequence alignment. Assembly gaps (N) in the reference sequence were replaced with the consensus sequence and mis-assemblies were either discarded (when only present in the reference but not in the consensus sequence) or included (when only present in the consensus but not in the reference sequence).

    Article Snippet: Sequencing Long-amplicon sequencing was performed with MinION (Oxford Nanopore Technologies Ltd)—a nanopore-based sequencing technology capable of producing read length s of up to 200 kb , , facilitating continuous sequencing across the entire mrjp cluster region.

    Techniques: Amplification, Sequencing, Derivative Assay