Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome
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{"title"=>"Selecting superior de novo transcriptome assemblies: Lessons learned by leveraging the best plant genome", "type"=>"journal", "authors"=>[{"first_name"=>"Loren A.", "last_name"=>"Honaas", "scopus_author_id"=>"6504270757"}, {"first_name"=>"Eric K.", "last_name"=>"Wafula", "scopus_author_id"=>"54789232300"}, {"first_name"=>"Norman J.", "last_name"=>"Wickett", "scopus_author_id"=>"8612138000"}, {"first_name"=>"Joshua P.", "last_name"=>"Der", "scopus_author_id"=>"8700144100"}, {"first_name"=>"Yeting", "last_name"=>"Zhang", "scopus_author_id"=>"55109794900"}, {"first_name"=>"Patrick P.", "last_name"=>"Edger", "scopus_author_id"=>"35078331000"}, {"first_name"=>"Naomi S.", "last_name"=>"Altman", "scopus_author_id"=>"55842734300"}, {"first_name"=>"J.", "last_name"=>"Chris Pires", "scopus_author_id"=>"56007587800"}, {"first_name"=>"James H.", "last_name"=>"Leebens-Mack", "scopus_author_id"=>"35314840500"}, {"first_name"=>"Claude W.", "last_name"=>"DePamphilis", "scopus_author_id"=>"55664042900"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"607586000", "sgr"=>"84953896612", "pmid"=>"26731733", "scopus"=>"2-s2.0-84953896612", "doi"=>"10.1371/journal.pone.0146062", "issn"=>"19326203"}, "id"=>"8100e08a-2e4a-3be2-816c-3e3067c7c72b", "abstract"=>"Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation.", "link"=>"http://www.mendeley.com/research/selecting-superior-novo-transcriptome-assemblies-lessons-learned-leveraging-best-plant-genome", "reader_count"=>163, "reader_count_by_academic_status"=>{"Unspecified"=>9, "Professor > Associate Professor"=>5, "Researcher"=>47, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>46, "Student > Postgraduate"=>5, "Student > Master"=>27, "Other"=>3, "Student > Bachelor"=>10, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>9, "Professor > Associate Professor"=>5, "Researcher"=>47, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>46, "Student > Postgraduate"=>5, "Student > Master"=>27, "Other"=>3, "Student > Bachelor"=>10, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Unspecified"=>11, "Biochemistry, Genetics and Molecular Biology"=>32, "Agricultural and Biological Sciences"=>110, "Chemistry"=>1, "Computer Science"=>5, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>110}, "Computer Science"=>{"Computer Science"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>32}, "Unspecified"=>{"Unspecified"=>11}}, "reader_count_by_country"=>{"New Zealand"=>1, "Canada"=>1, "Argentina"=>1, "Czech Republic"=>1, "Netherlands"=>1, "United States"=>2, "Malaysia"=>1, "Slovenia"=>2, "Spain"=>2}, "group_count"=>3}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2621211"], "description"=>"<p>Coverage of all detected genes by sequencing reads. The darkest bar represents the number of detected genes not tagged, and each progressively lighter bar represents genes in a bin with a 5% increase in coverage, with the two lightest bars showing the number of genes covered at >90% and >99%, respectively. Normalized BR12 = Normalized Illumina library from pooled biological replicates 1 and 2, BR12 = combined coverage of Illumina biological replicates 1 and 2, BR1 = Illumina biological replicate 1, BR2 = Illumina biological replicate 2.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633218, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illumina_Sequence_coverage_of_Arabidopsis_cDNAs_/1633218", "title"=>"Illumina Sequence coverage of <i>Arabidopsis</i> cDNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621212"], "description"=>"<p><i>SCE</i>RNA stands for <u>Sc</u>affolding and <u>E</u>rror correction for <i>de novo</i> assemblies of <u>RNA-Seq</u> data. This collection of post-processing tools allows flexible implementation at various steps post assembly and with multiple assemblers and data types.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633219, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SCE_RNA_Flowchart_/1633219", "title"=>"<i>SCE</i>RNA Flowchart.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621213"], "description"=>"<p>The histogram shows the magnitude (% change) and direction of change in each category for the Mosaik-S, CLC-S and Trinity-ICB assemblies of Illumina biological replicate 1. The post processed values in each category are printed above the x axis for each assembly. A vertical line separates categories where an assembly improvement would result in a decrease in the respective measure (“Expect Δ<0” categories, left of line) or an increase in the respective measure (“Expect Δ>0” categories, right of line).</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633220, "categories"=>["Uncategorised"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Post_processed_assembly_delta_plot_showing_the_effect_of_post_processing_in_several_assembly_quality_categories_/1633220", "title"=>"Post-processed assembly delta plot, showing the effect of post-processing in several assembly quality categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621214"], "description"=>"<p>The units for “Assembly Quality” are Normalized Bit Score (BS, maximum of 2) and the units of “Sequence Depth” are Sequenced Fragments/bp (SFB). The number printed in the plot area is the number of unigenes with normalized bit score above 1.5. A BS of 1.5 is an arbitrary threshold, yet represents long and accurate assemblies (75% length, high accuracy), and is used to illustrate the difference in the high-density region seen in most plots near BS 1.75–2.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633221, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_quality_of_unigenes_as_a_function_of_sequencing_depth_for_Illumina_biological_replicate_1_/1633221", "title"=>"The quality of unigenes as a function of sequencing depth for Illumina biological replicate 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621215"], "description"=>"<p>The units for “Assembly Quality” are Normalized Bit Score (BS) and the units for “Sequence Depth” are Sequenced Fragments/bp (SFB). The number printed in the plot area is the number of unigenes with normalized bit score above 1.5. A BS of 1.5 is an arbitrary threshold and is used to illustrate the differences in the high-density region seen in most plots near BS 1.75–2.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633222, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Normalization_improves_the_recovery_rate_of_highly_expressed_genes_compare_to_Fig_4_/1633222", "title"=>"Normalization improves the recovery rate of highly expressed genes (compare to Fig 4).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621216"], "description"=>"<p>Reads were mapped to post-processed assemblies of biological replicate 1. The number of reads (X axis) that map to an assembly are an indicator of assembly completeness and quality, while the incidence of new tags (Y axis) indicates how completely the assembly reflects the diversity present in the read data.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633223, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Read_titration_analysis_/1633223", "title"=>"Read titration analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621217"], "description"=>"<p>The use of UCOs as a proxy for the transcriptome assembly helps to identify leading assemblies when considered with the read titration curve analysis. When considered together, Trinity-ICB, which was the clear leader in our reference-based analyses, is also selected as the leader by the reference-<i>independent</i> metrics.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633224, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ultra_conserved_orthologs_UCO_coverage_in_post_processed_assemblies_of_BR1_/1633224", "title"=>"Ultra-conserved orthologs (UCO) coverage in post-processed assemblies of BR1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621218"], "description"=>"<p>Illumina biological replicate 1 was subsampled to produce datasets of 1, 2, 3, and 4 Gbp. Replicate subsamples at 1 Gbp (top row) show reproducible results. Increasing the data by 1 Gbp to 2, 3, and 4 show diminishing increases in well assembled (>1.5BS) genes. The 4 Gbp subsampled assembly showed highly similar results to the biological replicate datasets. Doubling the data volume (BR12) produced a small increase in well assembled genes (>1.5BS) accompanied by a small increase in Type I mis-assembly. This analysis indicates 4 Gbp is a practical target data volume for <i>de novo</i> plant transcriptomes.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633225, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_4_Gbp_is_a_practical_target_volume_for_de_novo_transcriptome_assembly_/1633225", "title"=>"4 Gbp is a practical target volume for <i>de novo</i> transcriptome assembly.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621219"], "description"=>"<p>Considering the N<sub>50</sub> length, proportion of mappable reads, and UCO recovery we recapitulate the reference-dependent ranking of <i>de novo</i> assemblers.</p>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633226, "categories"=>["Biological Sciences"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. Leebens-Mack", "Claude W. dePamphilis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146062.g009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Integration_of_our_reference_independent_metrics_shows_the_top_3_are_closest_to_Mosaik_S_/1633226", "title"=>"Integration of our reference-independent metrics shows the top 3 are closest to Mosaik-<i>S</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 14:26:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/2621239", "https://ndownloader.figshare.com/files/2621240", "https://ndownloader.figshare.com/files/2621241", "https://ndownloader.figshare.com/files/2621242", "https://ndownloader.figshare.com/files/2621243", "https://ndownloader.figshare.com/files/2621244", "https://ndownloader.figshare.com/files/2621245", "https://ndownloader.figshare.com/files/2621246", "https://ndownloader.figshare.com/files/2621247", "https://ndownloader.figshare.com/files/2621248", "https://ndownloader.figshare.com/files/2621249", "https://ndownloader.figshare.com/files/2621250", "https://ndownloader.figshare.com/files/2621251", "https://ndownloader.figshare.com/files/2621252", "https://ndownloader.figshare.com/files/2621253", "https://ndownloader.figshare.com/files/2621254", "https://ndownloader.figshare.com/files/2621255", "https://ndownloader.figshare.com/files/2621256", "https://ndownloader.figshare.com/files/2621257", "https://ndownloader.figshare.com/files/2621258", "https://ndownloader.figshare.com/files/2621259", "https://ndownloader.figshare.com/files/2621260", "https://ndownloader.figshare.com/files/2621261", "https://ndownloader.figshare.com/files/2621262"], "description"=>"<div><p>Whereas <i>de novo</i> assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 <i>de novo</i> assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of <i>de novo</i> assemblies for <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i> transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of <i>de novo</i> transcriptome assemblies is best assessed through consideration of a <i>combination</i> of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N<sub>50</sub> length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce <i>SCE</i>RNA, a broadly applicable modular protocol for <i>de novo</i> assembly improvement. Finally, our <i>de novo</i> assembly of the <i>Arabidopsis</i> leaf transcriptome revealed ~20 putative <i>Arabidopsis</i> genes lacking in the current annotation.</p></div>", "links"=>[], "tags"=>["assembler", "benchmark Illumina transcriptome data", "SCERNA", "Oryza sativa transcriptomes", "Arabidopsis leaf transcriptome", "99 transcriptome assemblies", "Lessons Learned", "transcriptome assembly strategies", "Arabidopsis thaliana", "chimeric assemblies", "abundance transcripts", "clc", "Normalized libraries", "assembly improvement", "Superior De Novo Transcriptome Assemblies", "Controlled analyses", "transcriptome assemblies", "lack 1000", "Plant Genome", "Arabidopsis genes"], "article_id"=>1633238, "categories"=>["Uncategorised"], "users"=>["Loren A. Honaas", "Eric K. Wafula", "Norman J. Wickett", "Joshua P. Der", "Yeting Zhang", "Patrick P. Edger", "Naomi S. Altman", "J. Chris Pires", "James H. 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  • {"unique-ip"=>"53", "full-text"=>"56", "pdf"=>"10", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"43", "full-text"=>"46", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"28", "full-text"=>"32", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"10", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"28", "full-text"=>"36", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"27", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"69", "full-text"=>"88", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"26", "full-text"=>"23", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"23", "full-text"=>"31", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"31", "full-text"=>"35", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"40", "full-text"=>"54", "pdf"=>"9", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"25", "full-text"=>"36", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"25", "full-text"=>"18", "pdf"=>"9", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"21", "full-text"=>"15", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"24", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"16", "full-text"=>"12", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}

Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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