Read length versus Depth of Coverage for Viral Quasispecies Reconstruction
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{"title"=>"Read length versus Depth of Coverage for Viral Quasispecies Reconstruction", "type"=>"journal", "authors"=>[{"first_name"=>"Osvaldo", "last_name"=>"Zagordi", "scopus_author_id"=>"27268092100"}, {"first_name"=>"Martin", "last_name"=>"Däumer", "scopus_author_id"=>"6603872178"}, {"first_name"=>"Christian", "last_name"=>"Beisel", "scopus_author_id"=>"35374966400"}, {"first_name"=>"Niko", "last_name"=>"Beerenwinkel", "scopus_author_id"=>"9238131100"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84867060060", "pui"=>"365779582", "doi"=>"10.1371/journal.pone.0047046", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"23056573", "sgr"=>"84867060060"}, "id"=>"9fc7b285-fdc2-33b9-b40e-bffe3257c4cd", "abstract"=>"Recent advancements of sequencing technology have opened up unprecedented opportunities in many application areas. Virus samples can now be sequenced efficiently with very deep coverage to infer the genetic diversity of the underlying virus populations. Several sequencing platforms with different underlying technologies and performance characteristics are available for viral diversity studies. Here, we investigate how the differences between two common platforms provided by 454/Roche and Illumina affect viral diversity estimation and the reconstruction of viral haplotypes. Using a mixture of ten HIV clones sequenced with both platforms and additional simulation experiments, we assessed the trade-off between sequencing coverage, read length, and error rate. For fixed costs, short Illumina reads can be generated at higher coverage and allow for detecting variants at lower frequencies. They can also be sufficient to assess the diversity of the sample if sequences are dissimilar enough, but, in general, assembly of full-length haplotypes is feasible only with the longer 454/Roche reads. The quantitative comparison highlights the advantages and disadvantages of both platforms and provides guidance for the design of viral diversity studies.", "link"=>"http://www.mendeley.com/research/read-length-versus-depth-coverage-viral-quasispecies-reconstruction", "reader_count"=>81, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>22, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>15, "Other"=>1, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>22, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>2, "Student > Master"=>15, "Other"=>1, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>45, "Medicine and Dentistry"=>6, "Veterinary Science and Veterinary Medicine"=>2, "Social Sciences"=>1, "Computer Science"=>5, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>45}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Colombia"=>1, "Canada"=>1, "Sweden"=>1, "United States"=>1, "Brazil"=>2, "France"=>1, "Spain"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/565297"], "description"=>"<p>The plot shows the Shannon entropy of each column of the multiple sequence alignment of all mapped reads (orange bars) and its moving average in a window of 35 bp (blue lines). Numbering of bases follows the nucleotide position on the protease, i.e., position 1 corresponds to position 2253 on HXB2. As a reference, the top subfigure shows the diversity of the mixture of the original ten clones assuming equal frequencies. The remaining subfigures refer to the four sequencing experiments using either 454/Roche or Illumina GA and PCR amplification or not.</p>", "links"=>[], "tags"=>["protease"], "article_id"=>235791, "categories"=>["Virology", "Mathematics", "Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Osvaldo Zagordi", "Martin Daumer", "Christian Beisel", "Niko Beerenwinkel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0047046.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diversity_of_the_protease_region_measured_on_the_multiple_sequence_alignments_/235791", "title"=>"Diversity of the protease region measured on the multiple sequence alignments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 22:19:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/565363"], "description"=>"<p>The mean distance between clones of the underlying population was 7.5%. For global haplotype reconstruction, different conditions were tested, including varying read lengths (1st column: 36 bases, 2nd column: 75 bases, 3rd column: 150 bases), numbers of reads (1st row: 10,000, 2nd row: 20,000, 3rd row: 50,000), and sequencing error rates (grey: 0.01%, orange: 0.05%, blue: 0.1% per base). The y-axis reports reconstruction performance as the proportion close (φ<i><sub>q</sub></i>), defined as the fraction of reconstructed haplotypes that have at most <i>q</i> mismatches with respect to the original clones. The genomic region considered codes for amino acids 10 to 93 of the HIV protease.</p>", "links"=>[], "tags"=>["haplotype", "reconstruction"], "article_id"=>235859, "categories"=>["Virology", "Mathematics", "Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Osvaldo Zagordi", "Martin Daumer", "Christian Beisel", "Niko Beerenwinkel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0047046.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_haplotype_reconstruction_at_high_diversity_/235859", "title"=>"Global haplotype reconstruction at high diversity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 22:19:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/565464"], "description"=>"<p>Same as <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047046#pone-0047046-g002\" target=\"_blank\">Figure 2</a>, but the mean distance between clones is 1.9%.</p>", "links"=>[], "tags"=>["haplotype", "reconstruction"], "article_id"=>235952, "categories"=>["Virology", "Mathematics", "Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Osvaldo Zagordi", "Martin Daumer", "Christian Beisel", "Niko Beerenwinkel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0047046.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_haplotype_reconstruction_at_low_diversity_/235952", "title"=>"Global haplotype reconstruction at low diversity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-19 22:19:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/565565"], "description"=>"<p>For all four experiments, the total number of reads obtained and those overlapping amino acids 10 to 93 of the protease are reported. All 454/Roche reads mapping to this region were used in the haplotype reconstruction. For the Illumina Genome Analyzer, only those mapping to the region of highest entropy were considered. The last column reports mean and standard deviation of the sequencing error rate (1 – θ, where the parameter θ is estimated during haplotype reconstruction).</p>", "links"=>[], "tags"=>["sequencing"], "article_id"=>236058, "categories"=>["Virology", "Mathematics", "Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Osvaldo Zagordi", "Martin Daumer", "Christian Beisel", "Niko Beerenwinkel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0047046.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_of_sequencing_experiments_read_mapping_and_error_rates_/236058", "title"=>"Summary statistics of sequencing experiments, read mapping, and error rates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 22:20:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/565591"], "description"=>"<p>Reported are, for all four experiments, the relative frequencies in percent of the reconstructed haplotypes matching exactly one of the original clones (named 07-56681, …, 08-04512) as estimated by direct mapping and by ShoRAH. Undetected haplotypes are indicated by a dash (‘—’).</p>", "links"=>[], "tags"=>["reconstructed"], "article_id"=>236086, "categories"=>["Virology", "Mathematics", "Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Osvaldo Zagordi", "Martin Daumer", "Christian Beisel", "Niko Beerenwinkel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0047046.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequencies_of_all_perfectly_reconstructed_haplotypes_/236086", "title"=>"Frequencies of all perfectly reconstructed haplotypes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 22:20:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/565629"], "description"=>"<p>For all four experiments, we report the total number of predicted haplotypes (column Reconstructed), the number of correct haplotypes (true positives, TP), the number of reconstructed haplotypes that do not match any of the original clones (false positives, FP), and the number of missed haplotypes (false negatives, FN). This number is equal to 10 – TP, because ten is the total number of haplotypes present in the sample. Sensitivity is defined as TP/(TP+FN) and specificity as TP/(TP+FP). Local haplotype reconstruction was performed on the 252 bp region of the HIV <i>pol</i> gene coding for protease amino acids 10 to 93 for the 454/Roche data, and on the 35 bp subregion of highest entropy for the Illumina reads.</p>", "links"=>[], "tags"=>["haplotype"], "article_id"=>236119, "categories"=>["Virology", "Mathematics", "Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Osvaldo Zagordi", "Martin Daumer", "Christian Beisel", "Niko Beerenwinkel"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0047046.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_of_local_haplotype_reconstruction_/236119", "title"=>"Performance of local haplotype reconstruction.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-19 22:20:48"}

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Relative Metric

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