Skip to main content

Table 6 Simulated low coverage datasets analysis where the inputs of EIM pipeline are the read set and genome reconstructed by Bowtie2

From: Assessing the impact of exact reads on reducing the error rate of read mapping

Assembly Exact EIM (v2) Bowtie2   Exact EIM (v2) Bowtie2
DWGSIM simulator     ART simulator    
ReadSet5     ReadSet9    
Contigs-500 172 14 58   137 13 56
N50 (kbp) 43.9 735.7 159.6   75.2 909.5 175.3
Errors 0 53 64   1 45 53
IUPAC-codes 0 36 137   0 38 102
Genome-Fraction (%) 98.899 99.991 99.983   98.912 99.983 99.965
ReadSet6     ReadSet10    
Contigs-500 163 6 64   178 18 63
N50 (kbp) 44.4 1698.5 112.2   45.4 485.2 116.9
Errors 1 68 92   2 68 83
IUPAC-codes 0 28 95   0 39 187
Genome-Fraction (%) 98.843 99.998 99.976   98.871 99.988 99.984
ReadSet7     ReadSet11    
Contigs-500 424 11 55   425 17 70
N50 (kbp) 16.6 590.9 125.9   18 386.6 115.4
Errors 2 185 361   6 179 369
IUPAC-codes 0 24 117   0 38 151
Genome-Fraction (%) 98.666 99.993 99.985   98.697 99.989 99.983
ReadSet8     ReadSet12    
Contigs-500 397 17 56   366 13 49
N50 (kbp) 18.9 493.4 141.1   21.6 529.5 127.6
Errors 8 190 331   8 186 322
IUPAC-codes 0 21 105   0 23 121
Genome-Fraction (%) 98.771 99.99 99.979   98.799 99.983 99.982
  1. The evaluation metrics has been defined in the text. The columns headed ’Exact’, ’EIM (v2)’ and ’Bowtie2’ represent the contiguity and quality of contigs constructed by ExactMapping step of EIM, EIM (v2) and Bowtie2, respectively. The results of running the pipeline on datasets simulated by DWGSIM and ART are shown in left and right side of the table, respectively