Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps
Publication Date
March 19, 2008
Journal
PLOS ONE
Authors
Michael Roberts, Aleksey V. Zimin, Wayne Hayes, Brian R. Hunt, et al
Volume
3
Issue
3
Pages
e1836
DOI
http://doi.org/10.1371/journal.pone.0001836
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0001836
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/18350171
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266800
Europe PMC
http://europepmc.org/abstract/MED/18350171
Web of Science
000260762300037
Scopus
46649088769
Mendeley
http://www.mendeley.com/research/improving-phrapbased-assembly-rat-using-reliable-overlaps
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/934969"], "description"=>"<p>The correct positions of reads A, B, C and D are shown. (b) A “fork” in the overlaps. (c) a scenario where reads A and D have the same sequencing error at the same base.</p>", "links"=>[], "tags"=>["identifies", "genome", "contains", "copies"], "article_id"=>605400, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Michael Roberts", "Aleksey V. Zimin", "Wayne Hayes", "Brian R. Hunt", "Cevat Ustun", "James R. White", "Paul Havlak", "James Yorke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001836.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_the_technique_that_identifies_reliable_overlaps_a_a_scenario_where_a_genome_contains_two_copies_of_a_repeat_region_R_/605400", "title"=>"Illustration of the technique that identifies reliable overlaps: (a) a scenario where a genome contains two copies of a repeat region R.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:48:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/935121"], "description"=>"<p>The original Atlas assembly created two scaffolds only covering 73.2% of the finished sequence. Note the misplaced 20 Kb segment in the Atlas assembly. The UMD+Atlas assembly of GQQD correctly places the 20 Kb section originally misplaced and creates a single scaffold of the BAC covering 93.3% of the finished sequence. This UMD+Atlas assembly used reliable overlaps. This was the BAC that gave Atlas the most trouble.</p>", "links"=>[], "tags"=>["alignments", "assemblies", "finished", "bac"], "article_id"=>605563, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Michael Roberts", "Aleksey V. Zimin", "Wayne Hayes", "Brian R. Hunt", "Cevat Ustun", "James R. White", "Paul Havlak", "James Yorke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001836.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_alignments_of_assemblies_to_the_finished_sequence_of_BAC_GQQD_/605563", "title"=>"Two alignments of assemblies to the finished sequence of BAC GQQD.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:49:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/935298"], "description"=>"<p>The “original Atlas with UMD Plausible” and “original Atlas with UMD reliable” assembly results obtained by substituting Phrap for PhrapUMD with UMD plausible and reliable overlaps respectively. The best assembly (the bottom line) uses PhrapUMD and UMD reliable overlaps utilizing the 2-pass approach described in the “<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001836#s2\" target=\"_blank\">Methods</a>” section. It has almost 3% more sequence matching finished sequence than original Atlas with Phrap at less than 1/4 the original base error rate.</p>", "links"=>[], "tags"=>["assemblies", "subset", "21", "bacs"], "article_id"=>605733, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Michael Roberts", "Aleksey V. Zimin", "Wayne Hayes", "Brian R. Hunt", "Cevat Ustun", "James R. White", "Paul Havlak", "James Yorke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001836.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_three_assemblies_for_the_subset_of_the_21_BACs_from_the_Rat_genome_/605733", "title"=>"Comparison of the three assemblies for the subset of the 21 BACs from the Rat genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 10:50:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/935206"], "description"=>"<p>The original Atlas assembly created a single scaffold. The UMD+Atlas assembly of GMEZ assembled a 26 Kb section from the middle of the bigger scaffold into a separate Scaffold 1. Note that the large scaffold gap in the Scaffold 2 is estimated correctly. This UMD+Atlas assembly used reliable overlaps. This was the BAC that gave UMD+Atlas the most trouble and the only case where UMD+Atas assembly had two scaffolds.</p>", "links"=>[], "tags"=>["alignments", "assemblies", "finished", "bac"], "article_id"=>605647, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Michael Roberts", "Aleksey V. Zimin", "Wayne Hayes", "Brian R. Hunt", "Cevat Ustun", "James R. White", "Paul Havlak", "James Yorke"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001836.g003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_alignments_of_assemblies_to_the_finished_sequence_of_BAC_GMEZ_/605647", "title"=>"Two alignments of assemblies to the finished sequence of BAC GMEZ.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 10:49:48"}

PMC Usage Stats | Further Information

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Relative Metric

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