Table 2

Comparison of Minimus and phrap in the assembly of two bacterial genomes (Brucella suis and Staphylococcus aureus).

Genome

Genome size (Mbp)

# Reads/seq. coverage

Running time

# Contigs

N50 contig size (kbp)

coverage (%)

# errors

B. suis

3.3

36080

Minimus

6 m 30 s

110

43

99.9%

0

7.8

phrap

30 m 2 s

39

196

99.7%

8

S. aureus

2.9

49014

Minimus

16 m 40 s

85

51

99.8%

0

9.2

phrap

40 m

30

190

99.7%

5

Minimus ran faster than phrap and produced no errors. However, it generated a considerably 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.

Sommer et al. BMC Bioinformatics 2007 8:64   doi:10.1186/1471-2105-8-64