Skip to main content

Table 1 Statistics for the different mappers with mouse 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
bowtiePEunique91.8782399.979130.923.00583.36
bowtieSEunique92.0522499.922870.691.33311.38
bowtie2PEunique94.5788699.938021.2838.00572.58
bowtie2SEunique92.0828299.848451.1832.67294.64
Bwa alnPEunique94.6260299.887822.6615.67553.86
Bwa alnSEunique96.6087995.826121.853.00310.30
Bwa memPEunique94.5476399.957288.7719.33563.50
Bwa memSEunique92.0854899.896248.404.67299.76
novoalignPEunique95.5576099.614737.62226.33609.08
novoalignSEunique92.0898299.923077.6131.67315.96
STARPEunique95.3788299.8075316.672.00553.24
STARSEunique92.2334099.7300416.182.33285.06
bowtiePErandom99.9530093.672120.933.00596.75
bowtieSErandom99.9900193.041260.692.33317.67
bowtie2PErandom99.9999195.897371.2835.67607.86
bowtie2SErandom99.9809392.974061.1825.67324.26
Bwa alnPErandom99.9999895.942182.6617.67604.39
Bwa alnSErandom99.9980193.015311.854.00322.33
Bwa memPErandom99.9999895.940689.4218.33612.39
Bwa memSErandom99.9999893.010967.966.33329.82
novoalignPErandom99.9999895.848997.62272.00616.78
novoalignSErandom99.9998993.036977.6130.67322.72
STARPErandom99.9438095.9309416.675.00583.02
STARSErandom99.9902493.0192116.262.00314.19
bowtiePEmulti99.9530092.897190.9818.337289.52
bowtieSEmulti99.9900193.017110.719.672747.64
bowtie2PEmulti99.9999876.8065311.5328658.67228148.51
bowtie2SEmulti99.9999870.813918.748205.33161697.48
novoalignPEmulti99.9999895.859037.62307.672627.41
novoalignSEmulti99.9998993.037187.6199.003176.37
STARPEmulti99.9438095.9326523.957.002575.59
STARSEmulti99.9902493.0214326.644.002831.57
  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