IonCRAM: a reference-based compression tool for ion torrent sequence files

BMC Bioinformatics

Table 3 Space saving of Scramble and IonCRAM

File	Bam Size (GB)	CRAM Size (GB)	Scramble CRAM %saving of flow signal compared to BAM	Overall Scramble CRAM %Saving w.r.t. BAM	Naïve (Scramble + XZ/Zstd)	%saving Naïve	IonCRAM Size (GB)	IonCRAM %saving of flow signal compared to BAM	Overall IonCRAM %Saving w.r.t. BAM	Improvement over CRAM
Gene Panels
Average values for Gene Panels	1.55	1.02	33.03%	34.36%	1.28	17.11%	0.89	45.09%	42.60%	8.24%
Min values for Gene Panels	1.02	0.67	32.82%	34.00%	0.85	16.77%	0.59	44.73%	42.39%	7.46%
Max values for Gene Panels	2.76	1.82	33.23%	35.00%	2.28	17.44%	1.59	45.67%	42.90%	8.90%
In house Exomes
Average values for In house Exomes	57.07	36.85	33.37%	35.33%	48.61	18.19%	32.17	45.36%	43.59%	8.31%
Min	53.64	34.34	33.06%	35%	44.51	13.89%	30.31	44.97%	43.37%	7.49%
Max	60.25	38.87	33.61%	36%	51.88	22.36%	34.12	45.94%	43.90%	9.06%
Public Standard Exomes
Average values for public Exomes	42.39	29.01	29.05%	31.75%	36.57	13.71%	25.445	41.71%	39.84%	8.09%
Min	25.11	17.12	29.01%	31%	21.75	13.33%	14.99	41.34%	39.7%	7.80%
Max	50.60	34.67	29.09%	32%	43.72	14.55%	30.35	41.92%	40.0%	8.70%

Space saving of Scramble and IonCRAM for groups of test files. The second and third columns include the BAM and CRAM file sizes in GB, respectively. In Column 4, we show the saving in flow signal achieved by Scramble in the CRAM format. In Column 5, the overall space saving achieved by Scramble in the CRAM format compared to the original BAM file. Columns 6, 7, and 8 show the IonCRAM file size, percent saving in flow signals and overall saving, respectively. The final column compares overall percentage saving of IonCRAM compared to the respective CRAM files produced by Scramble.

ISSN: 1471-2105