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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.