Table 3 The descriptions of raw short-read sequences used in the evaluation experiments
From: Software for pre-processing Illumina next-generation sequencing short read sequences
| DataSet | Caenorhabditis elegans | Saccharomyces cerevisiae S288c | Escherichia coli O157 H7 |
|---|---|---|---|
| Taxonomy ID | 6239 | 559292 | 83334 |
| Reference Genome size (bp) | 100.3 M | 12.2 M | 5.5 M |
| #Chromosomes | 7* | 17* | 1 |
| SRA run | SRR065390 | SRR449310 | SRR957847 |
| Platform | Illumina Genome Analyzer II | Illumina HiSeq 2000 | Illumina MiSeq |
| Strategy | WGS | WGS | WGS |
| Source | Genomic | Genomic | Genomic |
| Layout | Paired | Paired | Paired |
| Read length | 100 | 76 | 150 |
| Nominal length | 356 | 230 | 350 |
| Total sequences (paired) | 33,808,546 | 1,898,259 | 2,241,778 |
| Total bases (paired) | 6,761,709,200 | 288,535,368 | 672,533,400 |
| Mean Phred quality score | 29.49 | 34.17 | 33.12 |
| Low Phred quality score (<=10) | 1,902,576 (2.81%) | 167,669 (4.42%) | 76,598 (1.71%) |
| Coverage | 67.4x | 23.7x | 122.3x |
| GC content (%) | 35 | 39 | 50 |