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Table 1 Runtime in CPU hours for each program on simulation 1 and 2

From: ContextMap 2: fast and accurate context-based RNA-seq mapping

Program Simulation 1 Simulation 2
ContextMap Bwt1 11.67 11.02
ContextMap Bwt2 (k=3, default) 16.47 15.58
ContextMap Bwt2 (k=10) 24.98 24.55
ContextMap Bwa 11.58 14.00
ContextMap Bwa ann 11.92 14.15
MapSplice 2 31.43 28.62
STAR 1-pass 0.82 1.28
STAR 1-pass ann 1.05 1.58
STAR 2-pass 9.60 10.28
STAR 2-pass ann 9.57 10.80
TopHat1 20.1 28.43
TopHat1 ann 20.53 29.03
TopHat2 25.17 27.23
TopHat2 ann 34.32 39.68
GSNAP 147.73 128.15
GSNAP ann 160.78 140.27
  1. All methods were run using 8 cores on the same machines and with the same parameter settings as in the RGASP evaluation [17]. ContextMap 2 with Bowtie 2 was run with the maximum number of alignments reported per read (k) set to 3 (default setting used for evaluating mapping quality) and 10, respectively. Runtime of STAR 2-pass includes the time required for running STAR 1-pass, indexing the genome with splice sites found in the first STAR run and re-running STAR.