Numbers of scaffolds.

Relationship Between Total Contig Length (Kbp) and Total Contig Number for the Scaffolded Bobwhite (Colinus virginianus) Genome (NB1.1).

Yvette A. Halley (534280)
Scot E. Dowd (107356)
Jared E. Decker (534281)
Paul M. Seabury (194366)
Eric Bhattarai (534282)
Charles D. Johnson (534283)
Dale Rollins (534284)
Ian R. Tizard (411122)
Donald J. Brightsmith (411118)
Markus J. Peterson (534285)
Jeremy F. Taylor (179789)
Christopher M. Seabury (194409)

March 2014

The y-axis represents total contig length, expressed in kilobase pairs (Kbp), and the x-axis repr...

Accession numbers of genome assemblies used in this study (see also S2 Table).

S. Widinugraheni (5879507)
J. Niño-Sánchez (5879510)
H. C. van der Does (5879513)
P. van Dam (5879516)
F. A. García-Bastidas (5879519)
S. Subandiyah (5879522)
H. J. G. Meijer (5879525)
H. C. Kistler (5879528)
G. H. J. Kema (5879531)
M. Rep (5879534)

October 2018

Accession numbers of genome assemblies used in this study (see also S2 Table).</p

Assembly statistics based on variable k-mer lengths.

Mark D. Huynh (746538)
Justin T. Page (494083)
Bryce A. Richardson (584202)
Joshua A. Udall (494082)

May 2015

Transcript assemblies based on variable k-mer lengths ranging from 35–127 in multiples of four of...

The number of genomic scaffolds anchored to the perennial grass genome assembly.

Cristiana Paina (615997)
Stephen L. Byrne (630395)
Bruno Studer (384950)
Odd Arne Rognli (2580124)
Torben Asp (34644)

March 2016

The number of genomic scaffolds anchored to the perennial grass genome assembly.</p

Scaffold Sizes

Jonathan A Eisen (187)
Robert S Coyne (274647)
Martin Wu (2823)
Dongying Wu (9076)
Mathangi Thiagarajan (126241)
Jennifer R Wortman (9068)
Jonathan H Badger (5511)
Qinghu Ren (12419)
Paolo Amedeo (81111)
Kristie M Jones (274648)
Luke J Tallon (12420)
Arthur L Delcher (3196)
Steven L Salzberg (190)
Joana C Silva (23647)
Brian J Haas (726)
William H Majoros (31774)
Maryam Farzad (9075)
Jane M Carlton (16085)
Roger K Smith Jr. (273033)
Jyoti Garg (219675)
Ronald E Pearlman (274649)
Kathleen M Karrer (274651)
Lei Sun (45752)
Gerard Manning (143099)
Nels C Elde (12122)
Aaron P Turkewitz (12126)
David J Asai (274653)
David E Wilkes (274654)
Yufeng Wang (274657)
Hong Cai (166815)
Kathleen Collins (24455)
B. Andrew Stewart (274659)
Suzanne R Lee (274660)
Katarzyna Wilamowska (274661)
Zasha Weinberg (48909)
Walter L Ruzzo (48911)
Dorota Wloga (274662)
Jacek Gaertig (248791)
Joseph Frankel (274663)
Che-Chia Tsao (274664)
Martin A Gorovsky (274665)
Patrick J Keeling (63315)
Ross F Waller (81235)
Nicola J Patron (62916)
J. Michael Cherry (5627)
Nicholas A Stover (274666)
Cynthia J Krieger (274667)
Christina del Toro (274668)
Hilary F Ryder (274670)
Sondra C Williamson (274671)
Rebecca A Barbeau (274673)
Eileen P Hamilton (274674)
Eduardo Orias (25047)

February 2013

<div>(A) Scaffold sizes versus MAC chromosome size. Blue diamonds represent scaffolds capped by t...

Size of pore width (Px) and pore height (Pz) for scaffolds with different numbers of layers; A1-A2) lattice scaffold, B1-B2) staggered scaffold (Data are presented as M ± SD).

Zahra Yazdanpanah (10038944)
Nitin Kumar Sharma (16548494)
Amanda Zimmerling (9636832)
David M. L. Cooper (4617442)
James D. Johnston (7371221)
Xiongbiao Chen (2862476)

July 2023

Size of pore width (Px) and pore height (Pz) for scaffolds with different numbers of layers; A1-A2) ...

Amount of penetration between subsequent printed layers; A) lattice scaffolds, B) staggered scaffolds (Data are presented as M ± SD).

Zahra Yazdanpanah (10038944)
Nitin Kumar Sharma (16548494)
Amanda Zimmerling (9636832)
David M. L. Cooper (4617442)
James D. Johnston (7371221)
Xiongbiao Chen (2862476)

July 2023

Amount of penetration between subsequent printed layers; A) lattice scaffolds, B) staggered scaffold...

Strand diameter and distance between strands for lattice and staggered scaffolds (Data are shown as M ± SD).

Zahra Yazdanpanah (10038944)
Nitin Kumar Sharma (16548494)
Amanda Zimmerling (9636832)
David M. L. Cooper (4617442)
James D. Johnston (7371221)
Xiongbiao Chen (2862476)

July 2023

Strand diameter and distance between strands for lattice and staggered scaffolds (Data are shown as ...

Assemblies obtained for three data sets: C. Microthrix, C. elegans, and human chromosome 14 (metrics calculated by QUAST).

Aleksandra Swiercz (3502541)
Wojciech Frohmberg (3167223)
Michal Kierzynka (5638562)
Pawel Wojciechowski (5638565)
Piotr Zurkowski (5638568)
Jan Badura (5638571)
Artur Laskowski (5638574)
Marta Kasprzak (3467243)
Jacek Blazewicz (3212577)

August 2018

Assemblies obtained for three data sets: C. Microthrix, C. elegans, and human chromosome 14 (metrics...

Values of NG(X) and the genome coverage as a function of the misassembled contigs length.

Aleksandra Swiercz (3502541)
Wojciech Frohmberg (3167223)
Michal Kierzynka (5638562)
Pawel Wojciechowski (5638565)
Piotr Zurkowski (5638568)
Jan Badura (5638571)
Artur Laskowski (5638574)
Marta Kasprzak (3467243)
Jacek Blazewicz (3212577)

August 2018

(A) Values of NG(X) for C. Microthrix data set. (B) Genome coverage and misassemblies for C. Microth...

Chap 3 - Appendix 2 - WGS statistics

Elsa Call

April 2020

WGS statistics from Chapter 3 "" Including: the number of scaffolds, assembly length, average scaff...

The total numbers of circular and elliptical nanoposts employed in the simulation domain in different densities.

You-Ren Hsu (1750426)
Ming-Chieh Lin (295075)
Hua-Kai Lin (5474444)
Yu-Hsu Chang (1560946)
Chih-Cheng Lu (3407114)
Hua-Yi Hsu (3278712)

July 2018

The total numbers of circular and elliptical nanoposts employed in the simulation domain in diffe...

Estimations of the number of beads per type to be integrated according to the lengths of the rows (cm).

Hala Alarashi (7321151)
Marion Benz (420130)
Julia Gresky (7321145)
Alice Burkhardt (16733874)
Andrea Fischer (691113)
Lionel Gourichon (578017)
Melissa Gerlitzki (16733877)
Martin Manfred (16733880)
Jorune Sakalauskaite (14698885)
Beatrice Demarchi (579317)
Meaghan Mackie (5471399)
Matthew Collins (279524)
Carlos P. Odriozola (5866295)
José Ángel Garrido Cordero (6664493)
Miguel Ángel Avilés (6664499)
Luisa Vigorelli (16733883)
Alessandro Re (11795270)
Hans Georg K. Gebel (7321157)

August 2023

Estimations of the number of beads per type to be integrated according to the lengths of the rows (c...

Scaffolding of the three data sets for the assemblers GRASShopPER, SOAPdenovo2, and SGA with the best combination of scaffolders SSPACE and SOAPdenovo2 (metrics calculated by QUAST).

Aleksandra Swiercz (3502541)
Wojciech Frohmberg (3167223)
Michal Kierzynka (5638562)
Pawel Wojciechowski (5638565)
Piotr Zurkowski (5638568)
Jan Badura (5638571)
Artur Laskowski (5638574)
Marta Kasprzak (3467243)
Jacek Blazewicz (3212577)

August 2018

Scaffolding of the three data sets for the assemblers GRASShopPER, SOAPdenovo2, and SGA with the bes...

The number of common UniqTag identifiers between build 75 of the Ensembl human genome and nine other builds, the number of common gene and protein identifiers between builds, and the number of genes with peptide sequences that are identical between builds.

Shaun D. Jackman (746366)
Joerg Bohlmann (280238)
İnanç Birol (5660038)

May 2015

The number of common UniqTag identifiers between build 75 of the Ensembl human genome and nine ot...

Relationship Between Total Contig Length (Kbp) and Total Contig Number for the Scaffolded Bobwhite (Colinus virginianus) Genome (NB1.1).

Yvette A. Halley (534280)
Scot E. Dowd (107356)
Jared E. Decker (534281)
Paul M. Seabury (194366)
Eric Bhattarai (534282)
Charles D. Johnson (534283)
Dale Rollins (534284)
Ian R. Tizard (411122)
Donald J. Brightsmith (411118)
Markus J. Peterson (534285)
Jeremy F. Taylor (179789)
Christopher M. Seabury (194409)

March 2014

The y-axis represents total contig length, expressed in kilobase pairs (Kbp), and the x-axis repr...

Accession numbers of genome assemblies used in this study (see also S2 Table).

S. Widinugraheni (5879507)
J. Niño-Sánchez (5879510)
H. C. van der Does (5879513)
P. van Dam (5879516)
F. A. García-Bastidas (5879519)
S. Subandiyah (5879522)
H. J. G. Meijer (5879525)
H. C. Kistler (5879528)
G. H. J. Kema (5879531)
M. Rep (5879534)

October 2018

Accession numbers of genome assemblies used in this study (see also S2 Table).</p

Assembly statistics based on variable k-mer lengths.

Mark D. Huynh (746538)
Justin T. Page (494083)
Bryce A. Richardson (584202)
Joshua A. Udall (494082)

May 2015

Transcript assemblies based on variable k-mer lengths ranging from 35–127 in multiples of four of...

The number of genomic scaffolds anchored to the perennial grass genome assembly.

Cristiana Paina (615997)
Stephen L. Byrne (630395)
Bruno Studer (384950)
Odd Arne Rognli (2580124)
Torben Asp (34644)

March 2016

The number of genomic scaffolds anchored to the perennial grass genome assembly.</p

Scaffold Sizes

Jonathan A Eisen (187)
Robert S Coyne (274647)
Martin Wu (2823)
Dongying Wu (9076)
Mathangi Thiagarajan (126241)
Jennifer R Wortman (9068)
Jonathan H Badger (5511)
Qinghu Ren (12419)
Paolo Amedeo (81111)
Kristie M Jones (274648)
Luke J Tallon (12420)
Arthur L Delcher (3196)
Steven L Salzberg (190)
Joana C Silva (23647)
Brian J Haas (726)
William H Majoros (31774)
Maryam Farzad (9075)
Jane M Carlton (16085)
Roger K Smith Jr. (273033)
Jyoti Garg (219675)
Ronald E Pearlman (274649)
Kathleen M Karrer (274651)
Lei Sun (45752)
Gerard Manning (143099)
Nels C Elde (12122)
Aaron P Turkewitz (12126)
David J Asai (274653)
David E Wilkes (274654)
Yufeng Wang (274657)
Hong Cai (166815)
Kathleen Collins (24455)
B. Andrew Stewart (274659)
Suzanne R Lee (274660)
Katarzyna Wilamowska (274661)
Zasha Weinberg (48909)
Walter L Ruzzo (48911)
Dorota Wloga (274662)
Jacek Gaertig (248791)
Joseph Frankel (274663)
Che-Chia Tsao (274664)
Martin A Gorovsky (274665)
Patrick J Keeling (63315)
Ross F Waller (81235)
Nicola J Patron (62916)
J. Michael Cherry (5627)
Nicholas A Stover (274666)
Cynthia J Krieger (274667)
Christina del Toro (274668)
Hilary F Ryder (274670)
Sondra C Williamson (274671)
Rebecca A Barbeau (274673)
Eileen P Hamilton (274674)
Eduardo Orias (25047)

February 2013

<div>(A) Scaffold sizes versus MAC chromosome size. Blue diamonds represent scaffolds capped by t...

Size of pore width (Px) and pore height (Pz) for scaffolds with different numbers of layers; A1-A2) lattice scaffold, B1-B2) staggered scaffold (Data are presented as M ± SD).

Zahra Yazdanpanah (10038944)
Nitin Kumar Sharma (16548494)
Amanda Zimmerling (9636832)
David M. L. Cooper (4617442)
James D. Johnston (7371221)
Xiongbiao Chen (2862476)

July 2023

Size of pore width (Px) and pore height (Pz) for scaffolds with different numbers of layers; A1-A2) ...

Amount of penetration between subsequent printed layers; A) lattice scaffolds, B) staggered scaffolds (Data are presented as M ± SD).

Zahra Yazdanpanah (10038944)
Nitin Kumar Sharma (16548494)
Amanda Zimmerling (9636832)
David M. L. Cooper (4617442)
James D. Johnston (7371221)
Xiongbiao Chen (2862476)

July 2023

Amount of penetration between subsequent printed layers; A) lattice scaffolds, B) staggered scaffold...

Strand diameter and distance between strands for lattice and staggered scaffolds (Data are shown as M ± SD).

Zahra Yazdanpanah (10038944)
Nitin Kumar Sharma (16548494)
Amanda Zimmerling (9636832)
David M. L. Cooper (4617442)
James D. Johnston (7371221)
Xiongbiao Chen (2862476)

July 2023

Strand diameter and distance between strands for lattice and staggered scaffolds (Data are shown as ...

Assemblies obtained for three data sets: C. Microthrix, C. elegans, and human chromosome 14 (metrics calculated by QUAST).

Aleksandra Swiercz (3502541)
Wojciech Frohmberg (3167223)
Michal Kierzynka (5638562)
Pawel Wojciechowski (5638565)
Piotr Zurkowski (5638568)
Jan Badura (5638571)
Artur Laskowski (5638574)
Marta Kasprzak (3467243)
Jacek Blazewicz (3212577)

August 2018

Assemblies obtained for three data sets: C. Microthrix, C. elegans, and human chromosome 14 (metrics...

Values of NG(X) and the genome coverage as a function of the misassembled contigs length.

Aleksandra Swiercz (3502541)
Wojciech Frohmberg (3167223)
Michal Kierzynka (5638562)
Pawel Wojciechowski (5638565)
Piotr Zurkowski (5638568)
Jan Badura (5638571)
Artur Laskowski (5638574)
Marta Kasprzak (3467243)
Jacek Blazewicz (3212577)

August 2018

(A) Values of NG(X) for C. Microthrix data set. (B) Genome coverage and misassemblies for C. Microth...

Chap 3 - Appendix 2 - WGS statistics

Elsa Call

April 2020

WGS statistics from Chapter 3 "" Including: the number of scaffolds, assembly length, average scaff...

The total numbers of circular and elliptical nanoposts employed in the simulation domain in different densities.

You-Ren Hsu (1750426)
Ming-Chieh Lin (295075)
Hua-Kai Lin (5474444)
Yu-Hsu Chang (1560946)
Chih-Cheng Lu (3407114)
Hua-Yi Hsu (3278712)

July 2018

The total numbers of circular and elliptical nanoposts employed in the simulation domain in diffe...

Estimations of the number of beads per type to be integrated according to the lengths of the rows (cm).

Hala Alarashi (7321151)
Marion Benz (420130)
Julia Gresky (7321145)
Alice Burkhardt (16733874)
Andrea Fischer (691113)
Lionel Gourichon (578017)
Melissa Gerlitzki (16733877)
Martin Manfred (16733880)
Jorune Sakalauskaite (14698885)
Beatrice Demarchi (579317)
Meaghan Mackie (5471399)
Matthew Collins (279524)
Carlos P. Odriozola (5866295)
José Ángel Garrido Cordero (6664493)
Miguel Ángel Avilés (6664499)
Luisa Vigorelli (16733883)
Alessandro Re (11795270)
Hans Georg K. Gebel (7321157)

August 2023

Estimations of the number of beads per type to be integrated according to the lengths of the rows (c...

Scaffolding of the three data sets for the assemblers GRASShopPER, SOAPdenovo2, and SGA with the best combination of scaffolders SSPACE and SOAPdenovo2 (metrics calculated by QUAST).

Aleksandra Swiercz (3502541)
Wojciech Frohmberg (3167223)
Michal Kierzynka (5638562)
Pawel Wojciechowski (5638565)
Piotr Zurkowski (5638568)
Jan Badura (5638571)
Artur Laskowski (5638574)
Marta Kasprzak (3467243)
Jacek Blazewicz (3212577)

August 2018

Scaffolding of the three data sets for the assemblers GRASShopPER, SOAPdenovo2, and SGA with the bes...

The number of common UniqTag identifiers between build 75 of the Ensembl human genome and nine other builds, the number of common gene and protein identifiers between builds, and the number of genes with peptide sequences that are identical between builds.

Shaun D. Jackman (746366)
Joerg Bohlmann (280238)
İnanç Birol (5660038)

May 2015

The number of common UniqTag identifiers between build 75 of the Ensembl human genome and nine ot...

Relationship Between Total Contig Length (Kbp) and Total Contig Number for the Scaffolded Bobwhite (Colinus virginianus) Genome (NB1.1).

Yvette A. Halley (534280)
Scot E. Dowd (107356)
Jared E. Decker (534281)
Paul M. Seabury (194366)
Eric Bhattarai (534282)
Charles D. Johnson (534283)
Dale Rollins (534284)
Ian R. Tizard (411122)
Donald J. Brightsmith (411118)
Markus J. Peterson (534285)
Jeremy F. Taylor (179789)
Christopher M. Seabury (194409)

March 2014

The y-axis represents total contig length, expressed in kilobase pairs (Kbp), and the x-axis repr...

Accession numbers of genome assemblies used in this study (see also S2 Table).

S. Widinugraheni (5879507)
J. Niño-Sánchez (5879510)
H. C. van der Does (5879513)
P. van Dam (5879516)
F. A. García-Bastidas (5879519)
S. Subandiyah (5879522)
H. J. G. Meijer (5879525)
H. C. Kistler (5879528)
G. H. J. Kema (5879531)
M. Rep (5879534)

October 2018

Accession numbers of genome assemblies used in this study (see also S2 Table).</p

Assembly statistics based on variable k-mer lengths.

Mark D. Huynh (746538)
Justin T. Page (494083)
Bryce A. Richardson (584202)
Joshua A. Udall (494082)

May 2015

Transcript assemblies based on variable k-mer lengths ranging from 35–127 in multiples of four of...

Numbers of scaffolds.

Abstract

Extracted data

Numbers of scaffolds.

Abstract

Extracted data

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