Reference-Free Validation of Short Read Data
Publication Date
September 22, 2010
Journal
PLOS ONE
Authors
Jan Schröder, James Bailey, Thomas Conway & Justin Zobel
Volume
5
Issue
9
Pages
e12681
DOI
https://dx.plos.org/10.1371/journal.pone.0012681
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0012681
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/20877643
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943903
Europe PMC
http://europepmc.org/abstract/MED/20877643
Web of Science
000282053100003
Scopus
77958453970
Mendeley
http://www.mendeley.com/research/referencefree-validation-short-read-data
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Reference-free validation of short read data", "type"=>"journal", "authors"=>[{"first_name"=>"Jan", "last_name"=>"Schröder", "scopus_author_id"=>"25723678000"}, {"first_name"=>"James", "last_name"=>"Bailey", "scopus_author_id"=>"7404350735"}, {"first_name"=>"Thomas", "last_name"=>"Conway", "scopus_author_id"=>"36629974600"}, {"first_name"=>"Justin", "last_name"=>"Zobel", "scopus_author_id"=>"7003595103"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-77958453970", "pui"=>"359826747", "doi"=>"10.1371/journal.pone.0012681", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "sgr"=>"77958453970", "pmid"=>"20877643"}, "id"=>"c8026c49-99ed-348c-848b-49f5eb7043ab", "abstract"=>"BACKGROUND: High-throughput DNA sequencing techniques offer the ability to rapidly and cheaply sequence material such as whole genomes. However, the short-read data produced by these techniques can be biased or compromised at several stages in the sequencing process; the sources and properties of some of these biases are not always known. Accurate assessment of bias is required for experimental quality control, genome assembly, and interpretation of coverage results. An additional challenge is that, for new genomes or material from an unidentified source, there may be no reference available against which the reads can be checked.\\n\\nRESULTS: We propose analytical methods for identifying biases in a collection of short reads, without recourse to a reference. These, in conjunction with existing approaches, comprise a methodology that can be used to quantify the quality of a set of reads. Our methods involve use of three different measures: analysis of base calls; analysis of k-mers; and analysis of distributions of k-mers. We apply our methodology to wide range of short read data and show that, surprisingly, strong biases appear to be present. These include gross overrepresentation of some poly-base sequences, per-position biases towards some bases, and apparent preferences for some starting positions over others.\\n\\nCONCLUSIONS: The existence of biases in short read data is known, but they appear to be greater and more diverse than identified in previous literature. Statistical analysis of a set of short reads can help identify issues prior to assembly or resequencing, and should help guide chemical or statistical methods for bias rectification.", "link"=>"http://www.mendeley.com/research/referencefree-validation-short-read-data", "reader_count"=>116, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>8, "Researcher"=>45, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>33, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>5, "Student > Bachelor"=>4, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>8, "Researcher"=>45, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>33, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>5, "Student > Bachelor"=>4, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>13, "Mathematics"=>1, "Agricultural and Biological Sciences"=>75, "Medicine and Dentistry"=>3, "Physics and Astronomy"=>2, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>13, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>75}, "Computer Science"=>{"Computer Science"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>9, "China"=>2, "Brazil"=>2, "Italy"=>1, "Australia"=>3, "France"=>1, "Switzerland"=>1, "Germany"=>1}, "group_count"=>5}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/828449"], "description"=>"<p>y-axis shows the total number of occurrences (log scale). Dotted lines represent the expected occurrences for the respective <i>k</i>-mer lengths. Poly-C sequences displayed as , poly-G as .</p>", "links"=>[], "tags"=>["poly-c", "poly-g", "sequences"], "article_id"=>498816, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Occurrences_of_poly_C_and_poly_G_sequences_of_different_length_depending_on_position_in_the_read_and_their_expected_values_for_read_set_/498816", "title"=>"Occurrences of poly-C and poly-G sequences of different length depending on position in the read and their expected values for read set .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:26:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/828677"], "description"=>"<p>*Values for linear correlation (better fit).</p>", "links"=>[], "tags"=>["coefficients", "polynucleotide", "sequences"], "article_id"=>499040, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cubic_correlation_coefficients_for_polynucleotide_sequences_of_different_length_for_the_read_set_/499040", "title"=>"Cubic correlation coefficients for polynucleotide sequences of different length for the read set .", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-22 02:30:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/828213"], "description"=>"<p>Basecalls for each position in the reads for dataset from the 1000 genomes project (see Section “Datasets”).</p>", "links"=>[], "tags"=>["reads", "dataset", "1000", "genomes"], "article_id"=>498582, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Basecalls_for_each_position_in_the_reads_for_dataset_from_the_1000_genomes_project_see_Section_Datasets_/498582", "title"=>"Basecalls for each position in the reads for dataset from the 1000 genomes project (see Section “Datasets”).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:23:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/828620"], "description"=>"<p>Data points correspond to , shown on the x-axis, on the y-axis. Note that the scale is not the same as used in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012681#pone-0012681-g005\" target=\"_blank\">Figure 5</a>.</p>", "links"=>[], "tags"=>["kl", "bootstrap"], "article_id"=>498988, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3d_plot_of_the_mean_KL_values_for_the_bootstrap_approach_simulated_data_/498988", "title"=>"3d plot of the mean KL values for the bootstrap approach (simulated data).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:29:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/413004", "https://ndownloader.figshare.com/files/413024", "https://ndownloader.figshare.com/files/413034", "https://ndownloader.figshare.com/files/413055", "https://ndownloader.figshare.com/files/413066", "https://ndownloader.figshare.com/files/413082", "https://ndownloader.figshare.com/files/413095", "https://ndownloader.figshare.com/files/413107", "https://ndownloader.figshare.com/files/413115", "https://ndownloader.figshare.com/files/413122", "https://ndownloader.figshare.com/files/413140", "https://ndownloader.figshare.com/files/413165", "https://ndownloader.figshare.com/files/413191", "https://ndownloader.figshare.com/files/413217", "https://ndownloader.figshare.com/files/413235", "https://ndownloader.figshare.com/files/413254", "https://ndownloader.figshare.com/files/413285"], "description"=>"<div><h3>Background</h3><p>High-throughput DNA sequencing techniques offer the ability to rapidly and cheaply sequence material such as whole genomes. However, the short-read data produced by these techniques can be biased or compromised at several stages in the sequencing process; the sources and properties of some of these biases are not always known. Accurate assessment of bias is required for experimental quality control, genome assembly, and interpretation of coverage results. An additional challenge is that, for new genomes or material from an unidentified source, there may be no reference available against which the reads can be checked.</p><h3>Results</h3><p>We propose analytical methods for identifying biases in a collection of short reads, without recourse to a reference. These, in conjunction with existing approaches, comprise a methodology that can be used to quantify the quality of a set of reads. Our methods involve use of three different measures: analysis of base calls; analysis of <em>k</em>-mers; and analysis of distributions of <em>k</em>-mers. We apply our methodology to wide range of short read data and show that, surprisingly, strong biases appear to be present. These include gross overrepresentation of some poly-base sequences, per-position biases towards some bases, and apparent preferences for some starting positions over others.</p><h3>Conclusions</h3><p>The existence of biases in short read data is known, but they appear to be greater and more diverse than identified in previous literature. Statistical analysis of a set of short reads can help identify issues prior to assembly or resequencing, and should help guide chemical or statistical methods for bias rectification.</p></div>", "links"=>[], "tags"=>["reference-free", "validation"], "article_id"=>141581, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0012681.s001", "https://dx.doi.org/10.1371/journal.pone.0012681.s002", "https://dx.doi.org/10.1371/journal.pone.0012681.s003", "https://dx.doi.org/10.1371/journal.pone.0012681.s004", "https://dx.doi.org/10.1371/journal.pone.0012681.s005", "https://dx.doi.org/10.1371/journal.pone.0012681.s006", "https://dx.doi.org/10.1371/journal.pone.0012681.s007", "https://dx.doi.org/10.1371/journal.pone.0012681.s008", "https://dx.doi.org/10.1371/journal.pone.0012681.s009", "https://dx.doi.org/10.1371/journal.pone.0012681.s010", "https://dx.doi.org/10.1371/journal.pone.0012681.s011", "https://dx.doi.org/10.1371/journal.pone.0012681.s012", "https://dx.doi.org/10.1371/journal.pone.0012681.s013", "https://dx.doi.org/10.1371/journal.pone.0012681.s014", "https://dx.doi.org/10.1371/journal.pone.0012681.s015", "https://dx.doi.org/10.1371/journal.pone.0012681.s016", "https://dx.doi.org/10.1371/journal.pone.0012681.s017"], "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Reference_Free_Validation_of_Short_Read_Data/141581", "title"=>"Reference-Free Validation of Short Read Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-09-22 00:26:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/828703"], "description"=>"<p>*In standard deviations.</p>", "links"=>[], "tags"=>["bootstrap"], "article_id"=>499072, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistics_for_the_bootstrap_approach_and_comparison_with_the_read_data_/499072", "title"=>"Statistics for the bootstrap approach and comparison with the read data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-22 02:31:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/828275"], "description"=>"<p>Bars represent the mean quality score for each position in a read (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012681#pone.0012681-Ewing1\" target=\"_blank\">[17]</a> for details).</p>", "links"=>[], "tags"=>["phred", "scores"], "article_id"=>498646, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_Phred_quality_scores_for_/498646", "title"=>"Average Phred quality scores for .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:24:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/828536"], "description"=>"<p>Data points correspond to , shown on the x-axis, on the y-axis.</p>", "links"=>[], "tags"=>["kl", "matrix"], "article_id"=>498905, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_3d_plot_of_the_KL_matrix_for_/498905", "title"=>"3d plot of the KL matrix for .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:28:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/828349"], "description"=>"<p>y-axis shows the total number of occurrences (log scale). Dotted lines represent the expected occurrences for the respective <i>k</i>-mer lengths. Poly-A sequences displayed as , poly-T as .</p>", "links"=>[], "tags"=>["poly-a", "poly-t", "sequences"], "article_id"=>498713, "categories"=>["Biological Sciences", "Medicine", "Genetics"], "users"=>["Jan Schröder", "James Bailey", "Thomas Conway", "Justin Zobel"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012681.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Occurrences_of_poly_A_and_poly_T_sequences_of_different_length_depending_on_position_in_the_read_and_their_expected_values_for_read_set_/498713", "title"=>"Occurrences of poly-A and poly-T sequences of different length depending on position in the read and their expected values for read set .", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-22 02:25:13"}

PMC Usage Stats | Further Information

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