InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

BMC Bioinformatics

Table 1 The summaries of assemblies on simulated metagenomic sim-113sp dataset

	Total cover length (Mbp)	Corr. N-len at 10 Mbp (bp)	E-size (bp)	Num. of covered genes	Total errors	Kbp/errors	Identity (%)
ABySS,k = 31	163.8	185,122	11,466	42,376	11,654	14.1	99.8
ABySS,k = 61	85.5	222,581	15,395	33,997	6,719	12.7	99.9
Bambus2	232.5	90,788	6,531	40,139	259,320	0.9	99.5
CABOG	244.8	139,195	10,142	47,968	2,482	98.6	99.8
IDBA-UD	227.9	222,631	14,651	67,713	5,416	42.1	99.7
MetaVelvet,k = 23	182.8	5,437	689	23,971	3,271	55.9	99.8
MetaVelvet,k = 61	76.3	121,245	8,628	26,747	251	304.1	99.9
Omega	75.8	90,383	7,751	25,837	78,078	0.9	99.8
Ray	90.2	35,059	2,365	22,958	45	2005.5	99.8
SOAPdenovo,k = 23	203.0	2,116	345	14,253	1,717	118.3	99.8
SOAPdenovo,k = 61	75.2	89,811	6,078	24,081	1,921	39.1	99.9
SPAdes	175.3	46,658	4,470	34,954	30,942	5.66	99.8
InteMAP	266.8	244,190	17,652	70,859	5,072	52.6	99.8

Only contigs with length ≥200 bp are considered. “k = 23”, “k = 31” and “k = 61” in the first column denote the assembler use the option of k-mer size at 23 bp, 31 bp and 61 bp. Bambus 2 uses unitigs from CABOG. Total cover length denotes the total length of reference sequences that are covered by contigs. Corr. N-len denotes the correct N-len size. E-size is also computed using correct contigs. Only complete covered genes are counted. Errors denote the structural errors in contigs. The error rate is measured as the average distance between errors. Identity denotes the average identity of the alignments between contigs and references, where unmapped segments of contigs are not considered. Values in bold indicate the best in the column

ISSN: 1471-2105