Table 1

Comparison of default and optimized CABOG assembly parameters

Default

Match

Relocation

Inversion

Redundancy

Coverage

Scaffold N50

Number of scaffolds


Arabidopsis thaliana

0.527

0.987

0.954

0.962

87.44%

117,128

57

Vitis vinifera

0.524

0.994

0.955

0.982

84.77%

114,280

60

Oryza sativa

0.535

0.992

0.966

0.982

88.49%

112,776

39

Populus trichocarpa

0.529

1.000

0.984

0.980

82.74%

134,082

65

Sorghum bicolor

0.542

0.889

0.944

0.956

86.58%

148,894

37

Zea mays

0.506

0.872

0.734

0.835

76.38%

52,719

140


Optimized

Match

Relocation

Inversion

Redundancy

Coverage

Scaffold N50

Number of scaffolds


Arabidopsis thaliana

0.645

0.996

0.996

0.979

99.86%

891,801

12

Vitis vinifera

0.694

0.993

0.953

0.992

99.46%

1,578,318

5

Oryza sativa

0.723

0.997

0.911

0.996

99.79%

1,785,140

6

Populus trichocarpa

0.813

1.000

1.000

0.997

99.16%

2,338,043

6

Sorghum bicolor

0.674

0.973

0.998

0.989

97.15%

663,137

11


Assembly evaluation scores and scaffold statistics determined for pseudomolecules created using 3 Mbp pools with 15x linear + 5x paired read coverage are shown for all of the genomes studied. Scores were determined using default and optimized assembly parameters, except for Z. mays that was only assembled using default parameters.

Haiminen et al. BMC Genomics 2011 12:194   doi:10.1186/1471-2164-12-194

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