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Table 2 Statistics for the different mappers with human chromosome 1 simulation data

From: Tools and best practices for retrotransposon analysis using high-throughput sequencing data

AlgorithmLibraryModeMapping percentageTrue Positive rateMemory in gbytesRunning Time in minutesOutput size in Mbytes
bowtiePEunique96.1272599.997031.074.00717.33
bowtieSEunique96.2677299.987600.801.67381.52
bowtie2PEunique97.5853099.991631.4236.00720.57
bowtie2SEunique96.2589799.936711.3325.33375.46
Bwa alnPEunique97.5860099.991353.0113.67703.84
Bwa alnSEunique98.4095898.526032.186.33381.22
Bwa memPEunique97.5766999.997455.658.33715.38
Bwa memSEunique96.2828599.980965.454.67379.88
novoalignPEunique97.8321199.991878.3199.67745.17
novoalignSEunique96.2879399.987558.3121.00385.94
STARPEunique97.7912999.9916618.122.33693.70
STARSEunique96.2980199.9622617.711.00363.12
bowtiePErandom99.9530697.787861.074.00722.46
bowtieSErandom99.9899397.486160.802.33383.45
bowtie2PErandom99.9996798.683781.4247.00738.73
bowtie2SErandom99.9706497.428611.3335.67391.06
Bwa alnPErandom99.9999898.687273.0113.67733.20
Bwa alnSErandom99.9981497.477042.187.33387.77
Bwa memPErandom99.9999898.692226.059.33744.88
Bwa memSErandom99.9999897.477105.263.00397.18
novoalignPErandom99.9999898.687978.31100.67748.47
novoalignSErandom99.9999897.487258.3127.67388.19
STARPErandom99.9435598.6876718.123.33709.61
STARSErandom99.9910397.4757817.702.00378.46
bowtiePEmulti99.9530697.414691.094.331032.87
bowtieSEmulti99.9899397.478880.822.00540.64
bowtie2PEmulti99.9999885.5568211.9271150.6781772.06
bowtie2SEmulti99.9999877.598956.3462006.33123387.84
novoalignPEmulti99.9999898.686988.3183.67800.39
novoalignSEmulti99.9999897.486018.3124.00572.07
STARPEmulti99.9435598.6906618.124.00754.66
STARSEmulti99.9910397.4792117.642.00541.40
  1. Values correspond to the average values of three independent simulated libraries with a 10X coverage. SE and PE refer to single end and paired end, respectively. Post-mapping filtering were applied for Bowtie2, Bwa mem and aln algorithms in order to extract uniquely-mapped reads