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Table 2 Comparison of assembly output with 454 reads and Illumina reads using different assemblers with different K-values.

From: A pilot study for channel catfish whole genome sequencing and de novo assembly

  Assembler K-value/Seed length N50 (bp) Maximum contig size (bp) Average contig size (bp) Number of contig
454   10 8,497 28,747 3,387 290
   11 7,524 28,723 3,457 284
   12 8,164 26,457 3,520 279
  Newbler 13 8,670 31,603 3,478 283
   14 8,635 28,741 3,523 279
   15 8,164 35,657 3,487 282
   16 8,674 28,736 3,486 282
   25 653 4,678 437 1,787
   35 736 3,717 468 1,645
   45 744 3,958 505 1,409
  Velvet 55 731 3,515 513 1,213
   65 718 2,730 556 943
   75 691 3,060 574 757
   85 621 3,538 584 622
   95 595 3,291 600 488
  MIRA   1,331 8,705 856 1,254
  CLC Genomics Workbench   1,239 7,621 988 1,220
Illumina   21 4,196 23,500 1,242 954
   25 5,678 40,818 1,495 809
   29 6,319 35,339 1,703 705
   33 4,745 32,597 1,744 659
   37 4,507 22,638 1,725 637
  Velvet 41 4,355 15,944 1,712 602
   45 3,619 19,463 1,677 579
   49 3,605 18,297 1,849 511
   53 3,381 18,243 1,813 518
   57 3,025 15,219 1,631 552
   61 3,388 15,148 2,011 390
   30 2,296 13,010 1,027 1,013
   35 2,493 16,400 1,132 933
   40 3,647 20,868 1,439 716
  ABySS 45 4,463 20,727 1,681 578
   50 5,481 22,931 2,084 453
   55 5,459 23,830 2,316 401
   60 6,870 22,594 2,496 386
   64 4,285 16,790 1,722 524
  CLC Genomics Workbench   823 8,964 454 3,572