Fast lossless compression via cascading Bloom filters

BMC Bioinformatics

Table 3 Performance comparison on high coverage values and read lengths longer than 100.

Time (sec)	coverage	quip	scalce	fastqz	BRC	quip -r	fastqz -r
	50	759	533	5426	1220	9544	4063
	100	1599	1016	10417	2211	20216	7479
	100, len 200	1280	1165	8760	1400	21705	7400
	200, len 400	2284	2518	15706	2209	51628	17769
Compression (bits/base)	50	2.0	0.62	0.97	0.43	0.34	0.32
	100	2.0	0.53	0.58	0.40	0.34	0.32
	100, len 200	1.8	0.43	0.61	0.37	0.19	0.45
	200, len 400	1.7	0.32	0.41	0.31	0.12	0.41

Reads were generated as described in the main text. Quip -r times include bt2 alignment.

ISSN: 1471-2105