QuorUM: An Error Corrector for Illumina Reads
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{"title"=>"QuorUM: An error corrector for Illumina reads", "type"=>"journal", "authors"=>[{"first_name"=>"Guillaume", "last_name"=>"Marçais", "scopus_author_id"=>"26530593700"}, {"first_name"=>"James A.", "last_name"=>"Yorke", "scopus_author_id"=>"7006469680"}, {"first_name"=>"Aleksey", "last_name"=>"Zimin", "scopus_author_id"=>"7004426833"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"605585905", "scopus"=>"2-s2.0-84939173793", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"26083032", "arxiv"=>"1307.351v1", "sgr"=>"84939173793", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0130821"}, "id"=>"dcfa5a9c-77b2-3d7c-8c8b-ec3bb311d89b", "abstract"=>"MOTIVATION: Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read at every base in the genome. These errors make handling the data more complicated because they result in a large number of low-count erroneous k-mers in the reads. However, there is enough information in the reads to correct most of the sequencing errors, thus making subsequent use of the data (e.g. for mapping or assembly) easier. Here we use the term \"error correction\" to denote the reduction in errors due to both changes in individual bases and trimming of unusable sequence. We developed an error correction software called QuorUM. QuorUM is mainly aimed at error correcting Illumina reads for subsequent assembly. It is designed around the novel idea of minimizing the number of distinct erroneous k-mers in the output reads and preserving the most true k-mers, and we introduce a composite statistic π that measures how successful we are at achieving this dual goal. We evaluate the performance of QuorUM by correcting actual Illumina reads from genomes for which a reference assembly is available.\\n\\nRESULTS: We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-core computing architectures and it is suitable for large data sets (1 billion bases checked and corrected per day per core). We also demonstrate that a third-party assembler (SOAPdenovo) benefits significantly from using QuorUM error-corrected reads. QuorUM error corrected reads result in a factor of 1.1 to 4 improvement in N50 contig size compared to using the original reads with SOAPdenovo for the data sets investigated.\\n\\nAVAILABILITY: QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at http://www.genome.umd.edu.\\n\\nCONTACT: gmarcais@umd.edu.", "link"=>"http://www.mendeley.com/research/quorum-error-corrector-illumina-reads", "reader_count"=>76, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>20, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>2, "Student > Master"=>12, "Other"=>3, "Student > Bachelor"=>2, "Lecturer"=>2, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>20, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>2, "Student > Master"=>12, "Other"=>3, "Student > Bachelor"=>2, "Lecturer"=>2, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Mathematics"=>2, "Agricultural and Biological Sciences"=>49, "Medicine and Dentistry"=>1, "Physics and Astronomy"=>1, "Computer Science"=>7, "Immunology and Microbiology"=>2, "Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>49}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>6, "Portugal"=>1, "Canada"=>1, "Czech Republic"=>1, "Sweden"=>1, "Netherlands"=>2, "Korea (South)"=>1, "China"=>1, "Taiwan"=>1, "Brazil"=>1, "France"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2120734"], "description"=>"<p>The solid lines represent the actual runtime while the dashed lines represent the perfect linear speed-up (except for HiTec which is not multi-threaded). The plot uses a log-log scale.</p>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452576, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130821.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Runtime_of_the_error_corrector_programs_on_Rhodobacter_vs_the_number_of_threads_/1452576", "title"=>"Runtime of the error corrector programs on Rhodobacter vs. the number of threads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-17 04:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2120736"], "description"=>"<p>The numbers for “false remain” and “true missing” in the table are percentages. We list the denominators used for the percentages in the headers of each of these columns. For the “false remain”, this denominator is the number of the false 31-mers in the original reads and for the “true missing”, it is the number of 31-mers in the reference. The “score” <i>π</i> = the product of the “false remain” and “true missing” columns. QuorUM’s <i>π</i> score is the best with a factor of 30, 15, and 3.5 better than the second best for Rhodobacter, Staphylococcus and Mouse C16 data sets respectively.</p>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452578, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130821.t001", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percent_of_false_31_mers_remaining_and_true_31_mers_missing_in_error_corrected_reads_/1452578", "title"=>"Percent of false 31-mers remaining and true 31-mers missing in error corrected reads.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-17 04:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2120737"], "description"=>"<p>Idealized contig size statistics (in kb).</p>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452579, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130821.t002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Idealized_contig_size_statistics_in_kb_/1452579", "title"=>"Idealized contig size statistics (in kb).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-17 04:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2120738"], "description"=>"<p>The number in parenthesis is the denominator used to compute the percentage, the number of original reads and the amount of sequence in the original reads respectively.</p>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452580, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130821.t003", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_the_original_reads_that_are_perfect_after_error_reduction_and_percentage_of_bases_contained_in_perfect_reads_compared_with_bases_in_original_reads_/1452580", "title"=>"Percentage of the original reads that are perfect after error reduction, and percentage of bases contained in perfect reads compared with bases in original reads.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-17 04:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2120739"], "description"=>"<p>Number of chimeric reads per 10000 after correction.</p>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452581, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130821.t004", "stats"=>{"downloads"=>5, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_chimeric_reads_per_10000_after_correction_/1452581", "title"=>"Number of chimeric reads per 10000 after correction.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-17 04:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2120740"], "description"=>"<p>The number of bases in each genome is reported in each column.</p>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452582, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130821.t005", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Runtime_of_each_program_in_hours_minutes_seconds_using_16_threads_and_memory_usage_in_giga_bytes_/1452582", "title"=>"Runtime of each program in hours:minutes:seconds, using 16 threads, and memory usage in giga-bytes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-17 04:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2120741"], "description"=>"<p>The “-d0” and “-d1” are parameters to SOAPdenovo instructing the assemblers to use all 31-mers or to ignore the 31-mers occurring only once. For MaSuRCA, which incorporates QuorUM, the result is in parentheses.</p>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452583, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130821.t006", "stats"=>{"downloads"=>11, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_assembled_NGA50_contig_size_in_kilo_bases_for_SOAPdenovo_/1452583", "title"=>"The assembled NGA50 contig size in kilo-bases for SOAPdenovo.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-17 04:40:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2120743", "https://ndownloader.figshare.com/files/2120744", "https://ndownloader.figshare.com/files/2120745", "https://ndownloader.figshare.com/files/2120746", "https://ndownloader.figshare.com/files/2120748"], "description"=>"<div><p>Motivation</p><p>Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read at every base in the genome. These errors make handling the data more complicated because they result in a large number of low-count erroneous <i>k</i>-mers in the reads. However, there is enough information in the reads to correct most of the sequencing errors, thus making subsequent use of the data (e.g. for mapping or assembly) easier. Here we use the term “error correction” to denote the reduction in errors due to both changes in individual bases and trimming of unusable sequence. We developed an error correction software called QuorUM. QuorUM is mainly aimed at error correcting Illumina reads for subsequent assembly. It is designed around the novel idea of minimizing the number of distinct erroneous <i>k</i>-mers in the output reads and preserving the most true <i>k</i>-mers, and we introduce a composite statistic π that measures how successful we are at achieving this dual goal. We evaluate the performance of QuorUM by correcting actual Illumina reads from genomes for which a reference assembly is available.</p><p>Results</p><p>We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-core computing architectures and it is suitable for large data sets (1 billion bases checked and corrected per day per core). We also demonstrate that a third-party assembler (SOAPdenovo) benefits significantly from using QuorUM error-corrected reads. QuorUM error corrected reads result in a factor of 1.1 to 4 improvement in N50 contig size compared to using the original reads with SOAPdenovo for the data sets investigated.</p><p>Availability</p><p>QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at <a href=\"http://www.genome.umd.edu\" target=\"_blank\">http://www.genome.umd.edu</a>.</p><p>Contact</p><p><a href=\"mailto:gmarcais@umd.edu\" target=\"_blank\">gmarcais@umd.edu</a>.</p></div>", "links"=>[], "tags"=>["sequencing errors", "100 bp", "N 50 contig size", "error correctors", "gpl", "Illumina Reads MotivationIllumina Sequencing data", "MaSuRCA assembly software", "source license", "novel idea", "QuorUM error", "statistic π", "error correction software", "reference assembly", "Error Corrector", "software package", "data sets investigated.AvailabilityQuorUM", "150 bp", "4 improvement"], "article_id"=>1452585, "categories"=>["Uncategorised"], "users"=>["Guillaume Marcais", "James A. Yorke", "Aleksey Zimin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0130821.s001", "https://dx.doi.org/10.1371/journal.pone.0130821.s002", "https://dx.doi.org/10.1371/journal.pone.0130821.s003", "https://dx.doi.org/10.1371/journal.pone.0130821.s004", "https://dx.doi.org/10.1371/journal.pone.0130821.s005"], "stats"=>{"downloads"=>10, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_QuorUM_An_Error_Corrector_for_Illumina_Reads_/1452585", "title"=>"QuorUM: An Error Corrector for Illumina Reads", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-17 04:40:35"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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