biobambam: tools for read pair collation based algorithms on BAM files

Table 3 Run-time comparison of bamtofastq and alternatives on compute farm nodes (part a)

Run-time comparison for BAM to FastQ conversion on server blades
Data set	Program	Memory/GB	Run-time/minutes
HG03520	biobambam	0.11	0.86±0.08
	bam2fastq	0.017	1.98±0.097
	bampe2fqworphans	0.0092	1.18±0.15
	Picard	0.62	3.86±0.23
	bamUtil	0.028	1.67±0.24
ERR239642	biobambam	0.13	1.55±0.15
	bam2fastq	0.033	3.89±0.12
	bampe2fqworphans	0.026	2.49±0.12
	Picard	0.76	7.45±0.27
	bamUtil	0.12	30.92±0.92
ERR217514	biobambam	0.13	3.86±0.27
	bam2fastq	0.080	9.52±0.35
	bampe2fqworphans	0.065	6.07±0.075
	Picard	0.95	18.83±0.44
	bamUtil	0.36	295.12±4.43
ERR196957	biobambam	0.13	6.17±0.37
	bam2fastq	0.13	17.74±0.45
	bampe2fqworphans	0.11	11.63±0.30
	Picard	1.14	33.99±0.79
	bamUtil	0.68	758.39±8.35
HG00096	biobambam	0.13	11.71±0.28
	bam2fastq	0.23	29.71±0.47
	bampe2fqworphans	0.032	16.87±0.22
	Picard	1.01	55.24±1.29
	bamUtil	0.23	25.50±1.14

Run-time comparison of biobambam’s bamtofastq, bam2fastq, bampe2fqworphans, Picard’s SamToFastQ and bamUtil’s bam2fastq for the data sets HG03520, ERR239642, ERR217514, ERR196957 and HG00096 described in Table2 on compute farm nodes.

ISSN: 1751-0473