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

From: InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

  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 = 61a 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
  1. 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
  2. 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
  3. bAssembly by SOAPdenovo was directly downloaded from the publication of [2]