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Table 3 Varying assembly parameters affects the length, number of scaffolds, and Sp185/333 genes present in different assemblies

From: An Sp185/333 gene cluster from the purple sea urchin and putative microsatellite-mediated gene diversification

    

Sp185/333

Assembly1

Unitigger rate (%)

Length (nt)2

Scaffolds

Genes

Gene Fragments

2

0.2

111,226

5

4

2

3

0.3

120,165

4

5

3

4

0.4

113,898

3

5

1

5

0.5

117,017

2

5

1

6

0.6

110,951

2

4

1

7

0.7

116,484

3

5

1

8

0.8

115,649

2

5

1

9

0.9

117,014

2

5

1

10

1.0

117,098

3

5

1

11

1.1

115,591

3

4

2

12

1.2

116,615

3

4

2

15

1.5

115,620

4

4

2

BCM-HGSC3

n/a

119,341

1

6

0

  1. 1Assemblies 2-15 were generated with the Celera Assembler [33].
  2. 2excluding gaps
  3. 3The sequence completed by BCM-HGSC (Genbank: AC204781.3) was assembled using Phrap [40] and Atlas [41].
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BMC Genomics

ISSN: 1471-2164

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