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

Teissandier, Aurélie; Servant, Nicolas; Barillot, Emmanuel; Bourc’his, Deborah

doi:10.1186/s13100-019-0192-1

Mobile DNA

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

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

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

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