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Table 1 Tools evaluated in this study

From: Impact of human gene annotations on RNA-seq differential expression analysis

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. 1 Abbreviations specified above are used in this study.
  2. 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. 3 Number of citations reported by the Web of Science in October 2019