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

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

  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
  1. 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