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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
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BMC Genomics

ISSN: 1471-2164

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