Table 1.
Tools evaluated in this study
| Tool | Abbrv. ∗1 | Version | Category ∗2 | #Citations ∗3 | References | Year |
|---|---|---|---|---|---|---|
| TopHat2 | Th | 2.1.1 | alignment | 11740 | [33, 34] | 2009 (ver.1), 2013 (ver.2) |
| STAR | Sr | 2.6.1d | alignment | 5443 | [28] | 2013 |
| HISAT | Hs | 2.1.0 | alignment | 1799 | [35, 36] | 2015 (ver.1), 2019 (ver.2) |
| Cufflinks | Cu | 2.2.1 | assembly, quantification, DE | 8102 | [37, 38] | 2010 (ver.1), 2013 (ver.2) |
| RSEM | Rs | 1.3.1 | quantification | 4335 | [25] | 2011 |
| StringTie | St | 2.0.6 | assembly, quantification | 721 | [39] | 2015 |
| Kallisto | Ka | 0.46.1 | quantification | 312 | [40] | 2016 |
| Salmon | Sa | 1.5.0 | quantification | 517 | [41] | 2017 |
| DESeq2 | De | 1.26.0 | DE | 6865 | [42, 43] | 2010 (ver.1), 2014 (ver.2) |
| EBSeq | Eb | 1.26.0 | DE | 468 | [44] | 2013 |
| Ballgown | Ba | 2.18.0 | DE | 102 | [45] | 2015 |
| Sleuth | Sl | 0.30.0 | DE | 170 | [46] | 2017 |
∗1 Abbreviations specified above are used in this study.
∗2 The category of tools indicates the following: alignment, tools to map RNA-seq reads to reference, quantification, tools to estimate abundances, DE, and tools to identify DEs using the statistical method.
∗3 Number of citations reported by the Web of Science in October 2019