Additional file 7: Table S4. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

Additional file 7: of De novo transcriptome assembly and analysis of Sf21 cells using illumina paired end sequencing

Pavan Kakumani (3461231)
Rohit Shukla (849851)
Vivek Todur (3461228)
Pawan Malhotra (33954)
Sunil Mukherjee (3461234)
Raj Bhatnagar (3461237)

August 2015

Abundance of identified unigenes: Abundance of the identified unigenes versus their respective lengt...

Additional file 9: of A comparative evaluation of hybrid error correction methods for error-prone long reads

Shuhua Fu (6295922)
Anqi Wang (782211)
Kin Au (6295925)

February 2019

Table S7. Performance statistics on improving de novo assembly. a. Genome assembly performance stati...

Additional file 8: Table S3. of Inferring synteny between genome assemblies: a systematic evaluation

Dang Liu (4808931)
Martin Hunt (188686)
Isheng Tsai (3584999)

January 2018

Assembly statistics among Caenorhabditis species and Strongyloides species including ALLMAPS results...

Additional file 5: Table S2. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

Nicolas Cerveau (3525029)
Daniel Jackson (176636)

December 2016

Assembly metrics of the three sub-assemblies and the final concatenated assembly for each of the six...

Additional file 6: Table S3. of Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Yuichiro Hara (3435893)
Kaori Tatsumi (3435890)
Michio Yoshida (3435896)
Eriko Kajikawa (3435887)
Hiroshi Kiyonari (106447)
Shigehiro Kuraku (2968)

November 2015

Completeness scores of transcriptome assemblies based on numbers of detected genes. (PDF 62Â kb

Additional file 7: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A2Zscores.txt: Zscores for all metrics and Overall Zscore for all metassemblies and input assemblies...

Additional file 3: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A1metricTable.txt: GAGE reported assembly evaluation metrics for all Assemblathon1 metassemblies at ...

Additional file 6: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A2metricTable.txt: REAPR, CEGMA and contiguity statistics reported for all Assemblathon2 metassembli...

Additional file 4: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A1Zscores.txt: Zscores for all metrics and Overall Zscore for all metassemblies and input assemblies...

Additional file 7: Table S6. of Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

Bhavya Papudeshi (4625437)
J. Haggerty (4625425)
Michael Doane (4625428)
Megan Morris (3407534)
Kevin Walsh (398980)
Douglas Beattie (4625434)
Dnyanada Pande (4625440)
Parisa Zaeri (4625431)
Genivaldo Silva (611816)
Fabiano Thompson (3631351)
Robert Edwards (1230)
Elizabeth Dinsdale (160062)

November 2017

Assembly evaluation parameters. List of all the assembly evaluation parameters. (DOCX 16Â kb

Additional file 3: of Comparative performance of transcriptome assembly methods for non-model organisms

Xin Huang (11077)
Xiao-Guang Chen (325128)
Peter Armbruster (3289887)

July 2016

Intersection of dipteran gene models identified by all four assembly strategies using the 180Â M dat...

Additional file 9: Table S4. of Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Yuichiro Hara (3435893)
Kaori Tatsumi (3435890)
Michio Yoshida (3435896)
Eriko Kajikawa (3435887)
Hiroshi Kiyonari (106447)
Shigehiro Kuraku (2968)

November 2015

Completeness assessment of comprehensive transcript sequence sets of bony vertebrates based on numbe...

Additional file 8: Figure S5. of Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Yuichiro Hara (3435893)
Kaori Tatsumi (3435890)
Michio Yoshida (3435896)
Eriko Kajikawa (3435887)
Hiroshi Kiyonari (106447)
Shigehiro Kuraku (2968)

November 2015

Completeness assessment of transcriptome assemblies by CEGMA and BUSCO referring to CVG. (PDF 468Â k...

Additional file 1: Table S1-S7. of Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing

Ting-Wen Chen (3574655)
Ruei-Chi Gan (3574652)
Yi-Feng Chang (195718)
Wei-Chao Liao (3574649)
Timothy Wu (1867861)
Chi-Ching Lee (519687)
Po-Jung Huang (38473)
Cheng-Yang Lee (2965686)
Yi-Ywan Chen (3574658)
Cheng-Hsun Chiu (8797)
Petrus Tang (8798)

August 2015

Table S1 – Summary of mapping reads to reference genome. Table S2 – Mismatch rates detected from rea...

Additional file 1: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

SupplementaryFile_v4.docx: Supplementary Notes, Figures, and Tables. (DOCX 795 kb

Additional file 7: of De novo transcriptome assembly and analysis of Sf21 cells using illumina paired end sequencing

Pavan Kakumani (3461231)
Rohit Shukla (849851)
Vivek Todur (3461228)
Pawan Malhotra (33954)
Sunil Mukherjee (3461234)
Raj Bhatnagar (3461237)

August 2015

Abundance of identified unigenes: Abundance of the identified unigenes versus their respective lengt...

Additional file 9: of A comparative evaluation of hybrid error correction methods for error-prone long reads

Shuhua Fu (6295922)
Anqi Wang (782211)
Kin Au (6295925)

February 2019

Table S7. Performance statistics on improving de novo assembly. a. Genome assembly performance stati...

Additional file 8: Table S3. of Inferring synteny between genome assemblies: a systematic evaluation

Dang Liu (4808931)
Martin Hunt (188686)
Isheng Tsai (3584999)

January 2018

Assembly statistics among Caenorhabditis species and Strongyloides species including ALLMAPS results...

Additional file 5: Table S2. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

Nicolas Cerveau (3525029)
Daniel Jackson (176636)

December 2016

Assembly metrics of the three sub-assemblies and the final concatenated assembly for each of the six...

Additional file 6: Table S3. of Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Yuichiro Hara (3435893)
Kaori Tatsumi (3435890)
Michio Yoshida (3435896)
Eriko Kajikawa (3435887)
Hiroshi Kiyonari (106447)
Shigehiro Kuraku (2968)

November 2015

Completeness scores of transcriptome assemblies based on numbers of detected genes. (PDF 62Â kb

Additional file 7: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A2Zscores.txt: Zscores for all metrics and Overall Zscore for all metassemblies and input assemblies...

Additional file 3: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A1metricTable.txt: GAGE reported assembly evaluation metrics for all Assemblathon1 metassemblies at ...

Additional file 6: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A2metricTable.txt: REAPR, CEGMA and contiguity statistics reported for all Assemblathon2 metassembli...

Additional file 4: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

A1Zscores.txt: Zscores for all metrics and Overall Zscore for all metassemblies and input assemblies...

Additional file 7: Table S6. of Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

Bhavya Papudeshi (4625437)
J. Haggerty (4625425)
Michael Doane (4625428)
Megan Morris (3407534)
Kevin Walsh (398980)
Douglas Beattie (4625434)
Dnyanada Pande (4625440)
Parisa Zaeri (4625431)
Genivaldo Silva (611816)
Fabiano Thompson (3631351)
Robert Edwards (1230)
Elizabeth Dinsdale (160062)

November 2017

Assembly evaluation parameters. List of all the assembly evaluation parameters. (DOCX 16Â kb

Additional file 3: of Comparative performance of transcriptome assembly methods for non-model organisms

Xin Huang (11077)
Xiao-Guang Chen (325128)
Peter Armbruster (3289887)

July 2016

Intersection of dipteran gene models identified by all four assembly strategies using the 180Â M dat...

Additional file 9: Table S4. of Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Yuichiro Hara (3435893)
Kaori Tatsumi (3435890)
Michio Yoshida (3435896)
Eriko Kajikawa (3435887)
Hiroshi Kiyonari (106447)
Shigehiro Kuraku (2968)

November 2015

Completeness assessment of comprehensive transcript sequence sets of bony vertebrates based on numbe...

Additional file 8: Figure S5. of Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Yuichiro Hara (3435893)
Kaori Tatsumi (3435890)
Michio Yoshida (3435896)
Eriko Kajikawa (3435887)
Hiroshi Kiyonari (106447)
Shigehiro Kuraku (2968)

November 2015

Completeness assessment of transcriptome assemblies by CEGMA and BUSCO referring to CVG. (PDF 468Â k...

Additional file 1: Table S1-S7. of Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing

Ting-Wen Chen (3574655)
Ruei-Chi Gan (3574652)
Yi-Feng Chang (195718)
Wei-Chao Liao (3574649)
Timothy Wu (1867861)
Chi-Ching Lee (519687)
Po-Jung Huang (38473)
Cheng-Yang Lee (2965686)
Yi-Ywan Chen (3574658)
Cheng-Hsun Chiu (8797)
Petrus Tang (8798)

August 2015

Table S1 – Summary of mapping reads to reference genome. Table S2 – Mismatch rates detected from rea...

Additional file 1: of Metassembler: merging and optimizing de novo genome assemblies

Alejandro Wences (3573449)
Michael Schatz (475909)

September 2015

SupplementaryFile_v4.docx: Supplementary Notes, Figures, and Tables. (DOCX 795 kb

Additional file 7: of De novo transcriptome assembly and analysis of Sf21 cells using illumina paired end sequencing

Pavan Kakumani (3461231)
Rohit Shukla (849851)
Vivek Todur (3461228)
Pawan Malhotra (33954)
Sunil Mukherjee (3461234)
Raj Bhatnagar (3461237)

August 2015

Abundance of identified unigenes: Abundance of the identified unigenes versus their respective lengt...

Additional file 9: of A comparative evaluation of hybrid error correction methods for error-prone long reads

Shuhua Fu (6295922)
Anqi Wang (782211)
Kin Au (6295925)

February 2019

Table S7. Performance statistics on improving de novo assembly. a. Genome assembly performance stati...

Additional file 8: Table S3. of Inferring synteny between genome assemblies: a systematic evaluation

Dang Liu (4808931)
Martin Hunt (188686)
Isheng Tsai (3584999)

January 2018

Assembly statistics among Caenorhabditis species and Strongyloides species including ALLMAPS results...

Additional file 7: Table S4. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

Abstract

Extracted data

Additional file 7: Table S4. of Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms

Abstract

Extracted data

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