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 | Â | Exact | EIM (v2) | Bowtie2 |
|---|---|---|---|---|---|---|---|
DWGSIM simulator | Â | Â | Â | ART simulator | Â | Â | Â |
ReadSet5 | Â | Â | Â | ReadSet9 | Â | Â | Â |
Contigs-500 | 172 | 14 | 58 | Â | 137 | 13 | 56 |
N50 (kbp) | 43.9 | 735.7 | 159.6 | Â | 75.2 | 909.5 | 175.3 |
Errors | 0 | 53 | 64 | Â | 1 | 45 | 53 |
IUPAC-codes | 0 | 36 | 137 | Â | 0 | 38 | 102 |
Genome-Fraction (%) | 98.899 | 99.991 | 99.983 | Â | 98.912 | 99.983 | 99.965 |
ReadSet6 | Â | Â | Â | ReadSet10 | Â | Â | Â |
Contigs-500 | 163 | 6 | 64 | Â | 178 | 18 | 63 |
N50 (kbp) | 44.4 | 1698.5 | 112.2 | Â | 45.4 | 485.2 | 116.9 |
Errors | 1 | 68 | 92 | Â | 2 | 68 | 83 |
IUPAC-codes | 0 | 28 | 95 | Â | 0 | 39 | 187 |
Genome-Fraction (%) | 98.843 | 99.998 | 99.976 | Â | 98.871 | 99.988 | 99.984 |
ReadSet7 | Â | Â | Â | ReadSet11 | Â | Â | Â |
Contigs-500 | 424 | 11 | 55 | Â | 425 | 17 | 70 |
N50 (kbp) | 16.6 | 590.9 | 125.9 | Â | 18 | 386.6 | 115.4 |
Errors | 2 | 185 | 361 | Â | 6 | 179 | 369 |
IUPAC-codes | 0 | 24 | 117 | Â | 0 | 38 | 151 |
Genome-Fraction (%) | 98.666 | 99.993 | 99.985 | Â | 98.697 | 99.989 | 99.983 |
ReadSet8 | Â | Â | Â | ReadSet12 | Â | Â | Â |
Contigs-500 | 397 | 17 | 56 | Â | 366 | 13 | 49 |
N50 (kbp) | 18.9 | 493.4 | 141.1 | Â | 21.6 | 529.5 | 127.6 |
Errors | 8 | 190 | 331 | Â | 8 | 186 | 322 |
IUPAC-codes | 0 | 21 | 105 | Â | 0 | 23 | 121 |
Genome-Fraction (%) | 98.771 | 99.99 | 99.979 | Â | 98.799 | 99.983 | 99.982 |