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Table 2 Average performance of aligners in mapping Ion Proton reads prepared by all the 2ug libraries (see Table 1 for details) to reference human genome and transcriptome

From: An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq

Aligner type Software Percentage of reads aligned to reference human
Genome Transcriptome
Unspliced Bowtie2 31.04 %
BWA 39.90 % 49.87 %
BWA-SW 93.25 % 82.28 %
TMAP 97.27 % 86.46 %
Subread 84.44 % ND*
Splice-aware Subjunc 85.99 % ND
TopHat2 75.70 % ND
TopHat2G 92.09 % ND
  1. *Not done