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 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

Algorithm	Library	Mode	Mapping percentage	True Positive rate	Memory in gbytes	Running Time in minutes	Output size in Mbytes
bowtie	PE	unique	91.87823	99.97913	0.92	3.00	583.36
bowtie	SE	unique	92.05224	99.92287	0.69	1.33	311.38
bowtie2	PE	unique	94.57886	99.93802	1.28	38.00	572.58
bowtie2	SE	unique	92.08282	99.84845	1.18	32.67	294.64
Bwa aln	PE	unique	94.62602	99.88782	2.66	15.67	553.86
Bwa aln	SE	unique	96.60879	95.82612	1.85	3.00	310.30
Bwa mem	PE	unique	94.54763	99.95728	8.77	19.33	563.50
Bwa mem	SE	unique	92.08548	99.89624	8.40	4.67	299.76
novoalign	PE	unique	95.55760	99.61473	7.62	226.33	609.08
novoalign	SE	unique	92.08982	99.92307	7.61	31.67	315.96
STAR	PE	unique	95.37882	99.80753	16.67	2.00	553.24
STAR	SE	unique	92.23340	99.73004	16.18	2.33	285.06
bowtie	PE	random	99.95300	93.67212	0.93	3.00	596.75
bowtie	SE	random	99.99001	93.04126	0.69	2.33	317.67
bowtie2	PE	random	99.99991	95.89737	1.28	35.67	607.86
bowtie2	SE	random	99.98093	92.97406	1.18	25.67	324.26
Bwa aln	PE	random	99.99998	95.94218	2.66	17.67	604.39
Bwa aln	SE	random	99.99801	93.01531	1.85	4.00	322.33
Bwa mem	PE	random	99.99998	95.94068	9.42	18.33	612.39
Bwa mem	SE	random	99.99998	93.01096	7.96	6.33	329.82
novoalign	PE	random	99.99998	95.84899	7.62	272.00	616.78
novoalign	SE	random	99.99989	93.03697	7.61	30.67	322.72
STAR	PE	random	99.94380	95.93094	16.67	5.00	583.02
STAR	SE	random	99.99024	93.01921	16.26	2.00	314.19
bowtie	PE	multi	99.95300	92.89719	0.98	18.33	7289.52
bowtie	SE	multi	99.99001	93.01711	0.71	9.67	2747.64
bowtie2	PE	multi	99.99998	76.80653	11.53	28658.67	228148.51
bowtie2	SE	multi	99.99998	70.81391	8.74	8205.33	161697.48
novoalign	PE	multi	99.99998	95.85903	7.62	307.67	2627.41
novoalign	SE	multi	99.99989	93.03718	7.61	99.00	3176.37
STAR	PE	multi	99.94380	95.93265	23.95	7.00	2575.59
STAR	SE	multi	99.99024	93.02143	26.64	4.00	2831.57

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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