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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