Short Barcodes for Next Generation Sequencing
Publication Date
December 30, 2013
Journal
PLOS ONE
Authors
Katharina Mir, Klaus Neuhaus, Martin Bossert & Steffen Schober
Volume
8
Issue
12
Pages
e82933
DOI
https://dx.plos.org/10.1371/journal.pone.0082933
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0082933
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24386128
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875435
Europe PMC
http://europepmc.org/abstract/MED/24386128
Web of Science
000329194700017
Scopus
84893527648
Mendeley
http://www.mendeley.com/research/short-barcodes-next-generation-sequencing
Events
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1331584"], "description"=>"<p>Transition probabilities (76-cycle Ga-II, phiX173, Bustard <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082933#pone.0082933-Kao1\" target=\"_blank\">[15]</a>).</p>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory", "probabilities", "bustard"], "article_id"=>888634, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082933.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transition_probabilities_76_cycle_Ga_II_phiX173_Bustard_15_/888634", "title"=>"Transition probabilities (76-cycle Ga-II, phiX173, Bustard [15]).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-30 02:44:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1331578"], "description"=>"<p>Illustration of codes having the same minimum distance but different distance distributions. The red dot represents the word sent, the black dot the received word , the blue dots are other codewords. In both cases, there is at least one code word with distance (hence the minimum distance). On the right hand side can be correctly decoded and assigned to , while on the left hand side is assigned to the wrong codeword (the closest blue dot below ).</p>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory"], "article_id"=>888628, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082933.g003", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Influence_of_distance_distribution_/888628", "title"=>"Influence of distance distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-30 02:44:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1331586", "https://ndownloader.figshare.com/files/1331587"], "description"=>"<div><p>We consider the design and evaluation of short barcodes, with a length between six and eight nucleotides, used for parallel sequencing on platforms where substitution errors dominate. Such codes should have not only good error correction properties but also the code words should fulfil certain biological constraints (<i>experimental parameters</i>). We compare published barcodes with codes obtained by two new constructions methods, one based on the currently best known linear codes and a simple randomized construction method. The evaluation done is with respect to the error correction capabilities, barcode size and their experimental parameters and fundamental bounds on the code size and their distance properties. We provide a list of codes for lengths between six and eight nucleotides, where for length eight, two substitution errors can be corrected. In fact, no code with larger minimum distance can exist.</p></div>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory", "barcodes"], "article_id"=>888636, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0082933.s001", "https://dx.doi.org/10.1371/journal.pone.0082933.s002"], "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Short_Barcodes_for_Next_Generation_Sequencing_/888636", "title"=>"Short Barcodes for Next Generation Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-12-30 02:44:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1331583"], "description"=>"<p>Addition and multiplication defined on {<i>A</i>,<i>C</i>,<i>G</i>,<i>T</i>}.</p>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory", "multiplication", "defined"], "article_id"=>888633, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082933.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Addition_and_multiplication_defined_on_A_C_G_T_/888633", "title"=>"Addition and multiplication defined on {<i>A</i>,<i>C</i>,<i>G</i>,<i>T</i>}.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-30 02:44:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1331581"], "description"=>"<p>Properties of barcode sets with fixed experimental constraints. The average () and the maximum error () are obtained over a non-symmetric channel defined in the <i>Channel Model</i> part.</p>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory", "barcode", "sets", "non-symmetric", "defined"], "article_id"=>888631, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082933.t004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Properties_of_barcode_sets_with_fixed_experimental_constraints_The_average_and_the_maximum_error_are_obtained_over_a_non_symmetric_channel_defined_in_the_Channel_Model_part_/888631", "title"=>"Properties of barcode sets with fixed experimental constraints. The average () and the maximum error () are obtained over a non-symmetric channel defined in the <i>Channel Model</i> part.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-30 02:44:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1331582"], "description"=>"<p>Algorithm RndBarcode.</p>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory"], "article_id"=>888632, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082933.t003", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Algorithm_RndBarcode_/888632", "title"=>"Algorithm RndBarcode.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-30 02:44:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1331580"], "description"=>"<p>Comparison of selected barcodes of length .</p>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory"], "article_id"=>888630, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082933.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distance_distribution_/888630", "title"=>"Distance distribution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-30 02:44:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/1331577"], "description"=>"<p>In the upper part of the figure the general model is shown, while in the lower part an example is depicted: In particular the messages consist of the numbers which are encoded using the code shown in the green box. In the example the number is encoded with the code word . On the receiver side, is received, which is decoded to the number . Notice, that this decoding procedure is only rational if we assume that one error is more likely than two errors.</p>", "links"=>[], "tags"=>["biotechnology", "Bioengineering", "Computational biology", "genomics", "Genome sequencing", "proteomics", "sequencing", "information science", "information theory", "theoretic"], "article_id"=>888627, "categories"=>["Biological Sciences", "Engineering", "Sociology"], "users"=>["Katharina Mir", "Klaus Neuhaus", "Martin Bossert", "Steffen Schober"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082933.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Communication_theoretic_model_/888627", "title"=>"Communication theoretic model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-30 02:44:43"}
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