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Table 1 Run time metrics of each method on 50 million paired-end reads of length 76 bp in an high performance computing cluster

From: Evaluation and comparison of computational tools for RNA-seq isoform quantification

 

Memory (Gb)

Run time (min)

Algorithm

Multi-thread

Cufflinks

3.5

117

ML

Yes

RSEM

5.6

154

ML

Yes

eXpress

0.55

30

ML

No

TIGAR2

28.3

1045

VB

Yes

kallisto

3.8

7

ML

Yes

Salmon

6.6

6

VB/ML

Yes

Salmon_aln

3

7

VB/ML

Yes

Sailfish

6.3

5

VB/ML

Yes

  1. For methods that support multi-threading, eight threads were used. For alignment-free methods (Kallisto, Salmon and Sailfish), a mapping step was included. The best performer in each category is underlined and the worst performer is in bold
  2. ML Maximum Likelihood, VB Variational Bayes
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BMC Genomics

ISSN: 1471-2164

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