From: Tools and best practices for retrotransposon analysis using high-throughput sequencing data
Algorithm | Library | Mode | Mapping percentage | True Positive rate | Memory in gbytes | Running Time in minutes | Output size in Mbytes |
---|---|---|---|---|---|---|---|
bowtie | PE | unique | 96.12725 | 99.99703 | 1.07 | 4.00 | 717.33 |
bowtie | SE | unique | 96.26772 | 99.98760 | 0.80 | 1.67 | 381.52 |
bowtie2 | PE | unique | 97.58530 | 99.99163 | 1.42 | 36.00 | 720.57 |
bowtie2 | SE | unique | 96.25897 | 99.93671 | 1.33 | 25.33 | 375.46 |
Bwa aln | PE | unique | 97.58600 | 99.99135 | 3.01 | 13.67 | 703.84 |
Bwa aln | SE | unique | 98.40958 | 98.52603 | 2.18 | 6.33 | 381.22 |
Bwa mem | PE | unique | 97.57669 | 99.99745 | 5.65 | 8.33 | 715.38 |
Bwa mem | SE | unique | 96.28285 | 99.98096 | 5.45 | 4.67 | 379.88 |
novoalign | PE | unique | 97.83211 | 99.99187 | 8.31 | 99.67 | 745.17 |
novoalign | SE | unique | 96.28793 | 99.98755 | 8.31 | 21.00 | 385.94 |
STAR | PE | unique | 97.79129 | 99.99166 | 18.12 | 2.33 | 693.70 |
STAR | SE | unique | 96.29801 | 99.96226 | 17.71 | 1.00 | 363.12 |
bowtie | PE | random | 99.95306 | 97.78786 | 1.07 | 4.00 | 722.46 |
bowtie | SE | random | 99.98993 | 97.48616 | 0.80 | 2.33 | 383.45 |
bowtie2 | PE | random | 99.99967 | 98.68378 | 1.42 | 47.00 | 738.73 |
bowtie2 | SE | random | 99.97064 | 97.42861 | 1.33 | 35.67 | 391.06 |
Bwa aln | PE | random | 99.99998 | 98.68727 | 3.01 | 13.67 | 733.20 |
Bwa aln | SE | random | 99.99814 | 97.47704 | 2.18 | 7.33 | 387.77 |
Bwa mem | PE | random | 99.99998 | 98.69222 | 6.05 | 9.33 | 744.88 |
Bwa mem | SE | random | 99.99998 | 97.47710 | 5.26 | 3.00 | 397.18 |
novoalign | PE | random | 99.99998 | 98.68797 | 8.31 | 100.67 | 748.47 |
novoalign | SE | random | 99.99998 | 97.48725 | 8.31 | 27.67 | 388.19 |
STAR | PE | random | 99.94355 | 98.68767 | 18.12 | 3.33 | 709.61 |
STAR | SE | random | 99.99103 | 97.47578 | 17.70 | 2.00 | 378.46 |
bowtie | PE | multi | 99.95306 | 97.41469 | 1.09 | 4.33 | 1032.87 |
bowtie | SE | multi | 99.98993 | 97.47888 | 0.82 | 2.00 | 540.64 |
bowtie2 | PE | multi | 99.99998 | 85.55682 | 11.92 | 71150.67 | 81772.06 |
bowtie2 | SE | multi | 99.99998 | 77.59895 | 6.34 | 62006.33 | 123387.84 |
novoalign | PE | multi | 99.99998 | 98.68698 | 8.31 | 83.67 | 800.39 |
novoalign | SE | multi | 99.99998 | 97.48601 | 8.31 | 24.00 | 572.07 |
STAR | PE | multi | 99.94355 | 98.69066 | 18.12 | 4.00 | 754.66 |
STAR | SE | multi | 99.99103 | 97.47921 | 17.64 | 2.00 | 541.40 |