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 | 39.90Â % | 49.87Â % | |
BWA-SW | 93.25Â % | 82.28Â % | |
TMAP | 97.27Â % | 86.46Â % | |
Subread | 84.44Â % | ND* | |
Splice-aware | Subjunc | 85.99Â % | ND |
TopHat2 | 75.70Â % | ND | |
TopHat2G | 92.09Â % | ND | |