Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling
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{"title"=>"Large scale loss of data in low-diversity illumina sequencing libraries can be recovered by deferred cluster calling", "type"=>"journal", "authors"=>[{"first_name"=>"Felix", "last_name"=>"Krueger", "scopus_author_id"=>"35740745100"}, {"first_name"=>"Simon R.", "last_name"=>"Andrews", "scopus_author_id"=>"8922760000"}, {"first_name"=>"Cameron S.", "last_name"=>"Osborne", "scopus_author_id"=>"7202987333"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "arxiv"=>"arXiv:1011.1669v3", "scopus"=>"2-s2.0-79551545281", "pui"=>"361204426", "doi"=>"10.1371/journal.pone.0016607", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "sgr"=>"79551545281", "pmid"=>"21305042"}, "id"=>"b28aa5fe-601e-3aa1-93cb-a8ebf00a6a4c", "abstract"=>"Massively parallel DNA sequencing is capable of sequencing tens of millions of DNA fragments at the same time. However, sequence bias in the initial cycles, which are used to determine the coordinates of individual clusters, causes a loss of fidelity in cluster identification on Illumina Genome Analysers. This can result in a significant reduction in the numbers of clusters that can be analysed. Such low sample diversity is an intrinsic problem of sequencing libraries that are generated by restriction enzyme digestion, such as e4C-seq or reduced-representation libraries. Similarly, this problem can also arise through the combined sequencing of barcoded, multiplexed libraries. We describe a procedure to defer the mapping of cluster coordinates until low-diversity sequences have been passed. This simple procedure can recover substantial amounts of next generation sequencing data that would otherwise be lost.", "link"=>"http://www.mendeley.com/research/large-scale-loss-data-lowdiversity-illumina-sequencing-libraries-recovered-deferred-cluster-calling", "reader_count"=>193, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>81, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>8, "Other"=>12, "Student > Master"=>15, "Student > Bachelor"=>9, "Lecturer"=>4, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>81, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>8, "Other"=>12, "Student > Master"=>15, "Student > Bachelor"=>9, "Lecturer"=>4, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Agricultural and Biological Sciences"=>138, "Veterinary Science and Veterinary Medicine"=>2, "Chemical Engineering"=>1, "Computer Science"=>4, "Earth and Planetary Sciences"=>1, "Engineering"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>24, "Mathematics"=>2, "Medicine and Dentistry"=>7, "Physics and Astronomy"=>3, "Social Sciences"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>3}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>3}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Engineering"=>{"Engineering"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>138}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>24}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Sweden"=>1, "Belgium"=>1, "United States"=>17, "Denmark"=>1, "Italy"=>1, "United Kingdom"=>3, "Chile"=>1, "Switzerland"=>1, "Germany"=>2, "India"=>1}, "group_count"=>7}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/802306"], "description"=>"<p>(a) The total number of sequences obtained from an unbiased PhiX control library processed with the SCS and GOAT pipelines. The number of reads returned by SCS analysis, commencing in cycle one was set to 100% and compared to GOAT pipeline-reprocessed raw image files, commencing in sequencing cycle five. (b) GOAT pipeline image analysis of three sample lanes with one initially biased sequence (IBS), comparing the number of sequences returned by analysis commencing in sequencing cycles one and five.</p>", "links"=>[], "tags"=>["cluster-calling", "increases", "low-diversity", "libraries"], "article_id"=>472673, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Felix Krueger", "Simon R. Andrews", "Cameron S. Osborne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016607.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Deferred_cluster_calling_increases_data_output_of_low_diversity_libraries_dramatically_/472673", "title"=>"Deferred cluster-calling increases data output of low-diversity libraries dramatically.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-28 00:44:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/802592"], "description"=>"<p>IBS: initially biased sequence; exp: independent experiment. Library origin was: 0 IBS -mouse, unbiased; 1 IBS - mouse, e4C; 2 IBS - yeast, 2 barcodes.</p>", "links"=>[], "tags"=>["libraries", "varying"], "article_id"=>472963, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Felix Krueger", "Simon R. Andrews", "Cameron S. Osborne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016607.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_yield_of_libraries_with_varying_degree_of_initial_sequence_bias_/472963", "title"=>"Sequence yield of libraries with varying degree of initial sequence bias.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-28 00:49:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/802355"], "description"=>"<p>(a) Simulated effect of increasing cluster densities on the number of usable sequences for samples containing varying amounts of low diversity (one to six initially biased sequences, IBS). The grey box marks a currently sensible range of cluster densities (equating to 125,000–300,000 clusters per tile on a GAIIx). (b) Percent increase in sequence data obtained by bareback-processing in relation to cluster density; libraries contained either one (n = 3), two (n = 4) or four (n = 1) different IBS tags.</p>", "links"=>[], "tags"=>["density-dependent", "avoided"], "article_id"=>472734, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Felix Krueger", "Simon R. Andrews", "Cameron S. Osborne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016607.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_and_cluster_density_dependent_data_loss_can_be_avoided_by_bareback_processing_/472734", "title"=>"Diversity- and cluster density-dependent data loss can be avoided by bareback-processing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-28 00:45:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/802459"], "description"=>"<p>(a) The percentage of sequences containing the expected initially biased sequence (IBS) identifiers, processed with either the standard SCS pipeline or subjected to bareback-processing, shuffling the first four bp to the end of the sequence. (b) Comparison of the sequencing depth in a 14 kb region for two- and four-IBS library samples after SCS- or bareback-processing, followed by sequence alignment. Each bar represents a window of 100 bp, and the heat map colours range between 20 and 500 sequencing reads. (c) Scatter plot representation comparing the read count distribution of SCS- vs. bareback-processed samples with either two or four different IBS. Reads of an entire flow-cell lane were counted in sliding windows of 100 bp.</p>", "links"=>[], "tags"=>["increases", "sequencing", "introducing"], "article_id"=>472827, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Felix Krueger", "Simon R. Andrews", "Cameron S. Osborne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016607.g004", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bareback_processing_increases_sequencing_depth_without_introducing_bias_/472827", "title"=>"Bareback-processing increases sequencing depth without introducing bias.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-28 00:47:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/802567"], "description"=>"<p>Sequence data were obtained from barcoded <i>Saccharomyces cerevisiae</i> libraries.</p>", "links"=>[], "tags"=>["scs", "bareback-processed"], "article_id"=>472941, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Felix Krueger", "Simon R. Andrews", "Cameron S. Osborne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016607.t002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_SCS_and_bareback_processed_data_/472941", "title"=>"Comparison of SCS and bareback-processed data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-28 00:49:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/400919", "https://ndownloader.figshare.com/files/400989"], "description"=>"<div><p>Massively parallel DNA sequencing is capable of sequencing tens of millions of DNA fragments at the same time. However, sequence bias in the initial cycles, which are used to determine the coordinates of individual clusters, causes a loss of fidelity in cluster identification on Illumina Genome Analysers. This can result in a significant reduction in the numbers of clusters that can be analysed. Such low sample diversity is an intrinsic problem of sequencing libraries that are generated by restriction enzyme digestion, such as e4C-seq or reduced-representation libraries. Similarly, this problem can also arise through the combined sequencing of barcoded, multiplexed libraries. We describe a procedure to defer the mapping of cluster coordinates until low-diversity sequences have been passed. This simple procedure can recover substantial amounts of next generation sequencing data that would otherwise be lost.</p> </div>", "links"=>[], "tags"=>["low-diversity", "illumina", "sequencing", "libraries", "recovered", "deferred", "calling"], "article_id"=>139214, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Felix Krueger", "Simon R. Andrews", "Cameron S. Osborne"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0016607.s001", "https://dx.doi.org/10.1371/journal.pone.0016607.s002"], "stats"=>{"downloads"=>10, "page_views"=>51, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Large_Scale_Loss_of_Data_in_Low_Diversity_Illumina_Sequencing_Libraries_Can_Be_Recovered_by_Deferred_Cluster_Calling/139214", "title"=>"Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-01-28 02:33:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/802218"], "description"=>"<p>(a) The total number of sequences per lane passing the purity filter step for samples with no bias, or one or two initially biased sequence (IBS) libraries. Data from three representative flow cell lanes are shown for each. (b) Current cluster-calling algorithms can discern clusters even at extremely high densities if the sequence composition during the first four cycles is unbiased. In low-diversity samples clusters with the same initially biased sequence in very close proximity may erroneously be called as a single cluster and may ultimately be removed by the purity filter.</p>", "links"=>[], "tags"=>["clusters", "illumina", "purity", "low-diversity"], "article_id"=>472591, "categories"=>["Molecular Biology", "Biological Sciences", "Genetics"], "users"=>["Felix Krueger", "Simon R. Andrews", "Cameron S. Osborne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016607.g001", "stats"=>{"downloads"=>3, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fewer_clusters_are_identified_by_the_Illumina_purity_filter_in_low_diversity_samples_/472591", "title"=>"Fewer clusters are identified by the Illumina purity filter in low-diversity samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-28 00:43:11"}

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Relative Metric

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