InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

BMC Bioinformatics

Table 3 Assembly statistics and predicted gene number on human gut microbial metagenome dataset (Sample MH0012)

	Sum of contig length (Mbp)	N-len at 5 Mbp (bp)	N-len at 50 Mbp (bp)	E-size (bp)	Non-redundant ORFs predicted	Num. of predicted complete ORFs
ABySS, k = 61^a	158.7	215,125	20,469	18,366	184,441	112,237
Bambus2	226.6	50,905	8,903	6,427	336,604	184,683
CABOG	185.6	46,459	12,738	6,964	222,638	119,907
IDBA-UD	277.2	177,468	41,831	23,970	339,336	186,427
MetaVelvet, k = 31	233.9	25,531	6,930	4,198	337,677	140,312
Omega	75.6	20,874	1,255	1,624	99,648	39,218
Ray	108.2	22,999	2,356	2,001	152,339	138,225
SOAPdenovo (Qin et al. 2010)^b	237.4	34,518	8,679	5,166	306,657	135,644
SPAdes	181.3	126,295	28,707	16,261	190,744	149,665
InteMAP	278.6	242,608	48,303	39,156	339,598	186,997

Only contigs ≥500 bp are considered. Bambus 2 uses unitigs from CABOG. “k = 31” denotes that MetaVelvet uses option of k-mer size 31. The assembly generated by Qin et al. (2010) is included, which is assembled by SOAPdenovo. In the column of non-redundant ORFs predicted, only ORFs ≥100 bp are counted. Last column lists the number of complete ORFs. The ORFs are predicted by MetaGeneMark [6]. Values in bold indicate the best in the column
^aAssembly by ABySS was generated from the correct reads from which many low coverage reads may be excluded because we failed ran ABySS on the mixed reads
^bAssembly by SOAPdenovo was directly downloaded from the publication of [2]

ISSN: 1471-2105