Skip to main content

Table 2 Comparison of Minimus and phrap in the assembly of two bacterial genomes (Brucella suis and Staphylococcus aureus).

From: Minimus: a fast, lightweight genome assembler

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
  1. 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.