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) | 100.3Â M | 12.2Â M | 5.5Â 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 |