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Table 1 Comparison of Minimus and phrap in the assembly of 10 mouse BACs from data obtained from the NCBI Trace Archive.

From: Minimus: a fast, lightweight genome assembler

BAC

BAC size (bp)

# Reads/seq. coverage

 

Running time

# Contigs

N50 contig size (kbp)

Coverage (%)

# errors

RP23-179K16

195,061

3685

Minimus

1 m 45 s

40

4.2

99.9

0

  

8

phrap

2 m 55 s

14

16.1

99.9

2

RP23-188E5

157,996

2983

Minimus

1 m 5 s

43

4.3

99.9

0

  

7

phrap

2 m 33 s

16

16.9

99.7

2

RP23-111A22

200,329

5428

Minimus

56 s

244

4.8

98.7

3

  

10

phrap

1 m 43 s

183

17

98.4

14

RP23-271013

239,837

7601

Minimus

3 m 11 s

448

1.5

100.0

2

  

14

phrap

6 m 30 s

329

6.3

98.6

10

RP23-283E4

178,084

5708

Minimus

3 m 49 s

713

1.4

99.9

2

  

15

phrap

9 m 53 s

467

3.9

98.7

8

RP23-286D16

195,068

4969

Minimus

41 s

90

9

99.9

2

  

8

phrap

1 m 22 s

264

40

99.9

5

RP23-296N18

187,242

1536

Minimus

36 s

52

6.5

99.9

0

  

6

phrap

1 m 5 s

34

16.1

99.0

12

RP23-319P12

190,514

5629

Minimus

1 m 39 s

131

4.9

99.9

3

  

14

phrap

2 m 29 s

139

18

98.0

18

RP23-363E23

199,409

5301

Minimus

1 m 19 s

111

5.5

99.9

3

  

12

phrap

2 m 12 s

178

20

100

15

RP23-425H1

188,835

1536

Minimus

14 s

46

10

97.2

1

  

6

phrap

38 s

28

21

98.4

5

  1. Minimus ran considerably faster than phrap and produced no errors, at the expense of a larger number of contigs. Note that the table contains two quantities denoted "coverage": the sequencing coverage (reported in the #Reads/seq. coverage column) represents the total amount of DNA in the sequenced reads, divided by the size of the chromosome, i.e. the redundancy in the sequenced data; the column headed "coverage" represents the fraction of the reference sequence covered by assembled contig. The latter measure does not take into account assembly errors, i.e. partial contig matches contribute to the overall coverage.