Table 2.
Real RNA-seq datasets taken from sequence read archive (SRA)
| SRA Study | Run accession | Run description | HPG Aligner |
HISAT |
STAR |
TopHat2 + Bowtie2 |
MapSplice |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RNM | CMR | Time | RNM | CMR | Time | RNM | CMR | Time | RNM | CMR | Time | RNM | CMR | Time | |||
| SRP009262 | SRR364003_1 | Illumina HiSeq 81 M 100 nt (single-end) | 4.53 | 79.72 | 11.0 | 15.16 | 76.10 | 10.43 | 5.50 | 75.00 | 13.9 | 25.73 | 63.38 | 115.9 | 4.63 | 76.83 | 139.9 |
| SRR364003_1 SRR364003_2 |
Illumina HiSeq 81 M 100 nt (paired-end) | 4.90 | 78.20 | 21.6 | 15.00 | 77.8 | 21.46 | 8.00 | 72.02 | 22.7 | 29.26 | 59.9 | 230.6 | 5.04 | 77.5 | 288.1 | |
| SRP003173 | SRR063344 SRR063345 |
Roche 454 GS FLX 1.26 M ∼600 nt (single-end) | 11.40 | 48.04 | 6.9 | 99.87 | 0.10 | 3.45 | 41.6 | 30.25 | 6.6 | 99.97 | 0.02 | 520.6 | NA | NA | NA |
SRA SRP009262 study was sequenced with Illumina HiSeq and contains 81.6 M reads (20 M reads are used for the benchmarking) of 100 nt length. Aligners were run in single and paired-end mode. SRA SRP003173 study was sequenced with Roche 454 GS FLX and contains 1.26 M reads (1,265,460) of ∼600 nt.
For each program, the table contains the following columns with the percentages of: RNM: reads not mapped; CMR: correctly mapped reads (mapped reads that cover the corresponding to known transcript positions). The last column, T, represents runtimes for producing a BAM file in min.