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Table 4 Summary of YH dataset assemblies

From: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Data and Program Version k-mer Scaffold total length (bp) Scaffold N50 (bp) Contig total length (bp) Contig N50 (bp) Coverage Time (h) Peak Memory at Graph Construction (G)
SOAPdenovo YH old data v1 25 2,837,024,602 455,380 2,327,931,678 4,933 80.51% 48^ 140
SOAPdenovo YH new data v1 31 2,901,125,426 5,806,495 2,661,982,498 12,709 81.16% 58^ 107
  v2 Multi-k-mer 45-61 2,905,148,690 22,297,138 2,799,723,051 20,926 93.91% 74^ 155
  v2 Sparse 35 2,874,598,201 18,033,622 2,767,141,367 18,856 93.17% 78^ 35
  v2 Sparse & Multi-k-mer 35-49 2,888,094,847 17,576,272 2,776,209,134 18,960 93.20% 81^ 35
ALLPATHS-LG§ YH new data 42807 96 2,809,141,261 16,195,684 2,600,792,533 31,101 88.53% 249* 343
  1. To be consistence with the result of ALLPATHS-LG, contigs and scaffolds shorter than 1 kb were filtered for SOAPdenovo assemblies.
  2. § Without ‘FixLocal’ due to the module failure (see Additional file1: Supplementary Method 7).
  3. ^ Time consumption including SOAPdenovo’s error correction, assembly and gap closure modules.
  4. * Time consumption including ALLPATHS-LG’s preparation and assembly modules.