Additional file 1: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Additional file 11: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S10. The summary of assemblies with Karect corrected short-reads and 40–50 kb long-reads. Lon...

Additional file 4: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S3. The summary of short-read-only and hybrid assemblies with SPAdes short-read correction. L...

Additional file 1: of Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

Margaret Staton (4676)
Tetyana Zhebentyayeva (3421250)
Bode Olukolu (3421247)
Guang Fang (3421244)
Dana Nelson (3421253)
John Carlson (4491)
Albert Abbott (4680)

October 2015

Symap-generated dot plots for chestnut physical and genetic map against plant reference genomes. (DO...

Additional file 2: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S2. Results of the Arabidopsis thaliana genome stepwise assembly by different assemblers using...

Additional file 4: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S4. Results of the Arabidopsis thaliana genome stepwise assembly by four different assemblers ...

Additional file 3: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S3. Sequencing libraries and generated sequence data used for the Larix sibirica genome assemb...

Additional file 6: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S6. The computing time taken to assemble each set and the complete Larix sibirica genome using...

Additional file 5: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S5. The traditional and stepwise CLC Assembly Cell genome assembly parameters for peach (Prunu...

Additional file 2: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S1. The summary of long-read-only assemblies. Long_5x indicates the 5x coverage of long-read ...

Additional file 1: of Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers

Eugeniya Bondar (6296057)
Yuliya Putintseva (4724973)
Nataliya Oreshkova (6296060)
Konstantin Krutovsky (4724994)

February 2019

Table S1. Genetic variants identified in the Siberian larch chloroplast genome. (XLSX 24 kb

Additional file 8: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S7. The summary of assemblies with Karect corrected short-reads and 10â20âkb long-reads. ...

Additional file 12: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S11. The summary of assemblies with Karect corrected short-reads and ≥ 50 kb long-reads. Long...

Additional file 2: Table S2. of Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

Erik Visser (3438095)
Jill Wegrzyn (141670)
Emma Steenkmap (3438092)
Alexander Myburg (3438098)
Sanushka Naidoo (2819755)

December 2015

Assembly statistics for EvidentialGene tr2aacds pipeline merged assembly compared to average statist...

Additional file 7: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S6. The summary of assemblies with Karect-corrected short-reads and ≤ 10 kb long-reads. Long ...

Additional file 3: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S2. The summary of short-read-only and hybrid assemblies with Karect short-read correction. L...

Additional file 11: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S10. The summary of assemblies with Karect corrected short-reads and 40–50 kb long-reads. Lon...

Additional file 4: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S3. The summary of short-read-only and hybrid assemblies with SPAdes short-read correction. L...

Additional file 1: of Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

Margaret Staton (4676)
Tetyana Zhebentyayeva (3421250)
Bode Olukolu (3421247)
Guang Fang (3421244)
Dana Nelson (3421253)
John Carlson (4491)
Albert Abbott (4680)

October 2015

Symap-generated dot plots for chestnut physical and genetic map against plant reference genomes. (DO...

Additional file 2: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S2. Results of the Arabidopsis thaliana genome stepwise assembly by different assemblers using...

Additional file 4: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S4. Results of the Arabidopsis thaliana genome stepwise assembly by four different assemblers ...

Additional file 3: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S3. Sequencing libraries and generated sequence data used for the Larix sibirica genome assemb...

Additional file 6: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S6. The computing time taken to assemble each set and the complete Larix sibirica genome using...

Additional file 5: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Dmitry Kuzmin (226311)
Sergey Feranchuk (4724979)
Vadim Sharov (4724985)
Alexander Cybin (6295673)
Stepan Makolov (6295676)
Yuliya Putintseva (4724973)
Natalya Oreshkova (6295679)
Konstantin Krutovsky (4724994)

February 2019

Table S5. The traditional and stepwise CLC Assembly Cell genome assembly parameters for peach (Prunu...

Additional file 2: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S1. The summary of long-read-only assemblies. Long_5x indicates the 5x coverage of long-read ...

Additional file 1: of Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers

Eugeniya Bondar (6296057)
Yuliya Putintseva (4724973)
Nataliya Oreshkova (6296060)
Konstantin Krutovsky (4724994)

February 2019

Table S1. Genetic variants identified in the Siberian larch chloroplast genome. (XLSX 24 kb

Additional file 8: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S7. The summary of assemblies with Karect corrected short-reads and 10â20âkb long-reads. ...

Additional file 12: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S11. The summary of assemblies with Karect corrected short-reads and ≥ 50 kb long-reads. Long...

Additional file 2: Table S2. of Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome

Erik Visser (3438095)
Jill Wegrzyn (141670)
Emma Steenkmap (3438092)
Alexander Myburg (3438098)
Sanushka Naidoo (2819755)

December 2015

Assembly statistics for EvidentialGene tr2aacds pipeline merged assembly compared to average statist...

Additional file 7: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S6. The summary of assemblies with Karect-corrected short-reads and ≤ 10 kb long-reads. Long ...

Additional file 3: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S2. The summary of short-read-only and hybrid assemblies with Karect short-read correction. L...

Additional file 11: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S10. The summary of assemblies with Karect corrected short-reads and 40–50 kb long-reads. Lon...

Additional file 4: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Weiwen Wang (740765)
Miriam Schalamun (6164342)
Alejandro Morales-Suarez (6164345)
David Kainer (6164348)
Benjamin Schwessinger (223005)
Robert Lanfear (395145)

December 2018

Figure S3. The summary of short-read-only and hybrid assemblies with SPAdes short-read correction. L...

Additional file 1: of Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

Margaret Staton (4676)
Tetyana Zhebentyayeva (3421250)
Bode Olukolu (3421247)
Guang Fang (3421244)
Dana Nelson (3421253)
John Carlson (4491)
Albert Abbott (4680)

October 2015

Symap-generated dot plots for chestnut physical and genetic map against plant reference genomes. (DO...

Additional file 1: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Abstract

Extracted data

Additional file 1: of Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

Abstract

Extracted data

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