MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression

BMC Bioinformatics

Table 2 Comparison of compression ratios of six software suites

Data	Original (MB)	MCH1 (MB)	MCH2 (MB)	MCG (MB)	MCEG (MB)	Align. %	Qual value (MB)	bzip2 (MB)	gzip (MB)	MFComp (MB)
ERR321482	1429	191	186	312	213	29.6	411	362	408	229
SRR359032	3981	319	282	657	458	61.8	2183	998	1133	263
ERR532393	8230	948	898	1503	1145	46.8	3410	2083	2366	1126
SRR1450398	5399	703	697	854	729	7.7	365	1345	1532	726
SRR062462	6478	137	135	188	144	2.7	153	222	356	161

For short hand notation, we used“MCH” = MetaCRAM-Huffman, “MCG” = MetaCRAM-Golomb, “MCEG” = MetaCRAM-extended Golomb, “MFComp” = MFCompress. MCH1 is the default option of MetaCRAM with Huffman encoding, and MCH2 is a version of MetaCRAM in which we removed the redundancy in both quality scores and the read IDs. “Align. %” refers to the total alignment rates from the first and second iteration. Minimum compressed file size achievable by the methods are written in bold case letters. Minimum compressed file size achievable by the methods are written in bold case letters

ISSN: 1471-2105