Table 2

Summary of assemblies generated using various de novo assemblers
Assemblies* No. of contigs ≥200bp No. of contigs with length ≥N50 No. of contigs with length ≥1kb Avg. contig length (bp) N50 (bp) Total size (Mbp)
CLC 217,114 29,564 33,332 658 1,120 142.8
ABySS 192,558 28,791 56,229 1,004 1,888 193.5
Velvet 311,734 56,471 42,685 580 809 181.0
Final merged 370,798 48,730 68,569 743 1,395 275.5

*CLC denotes the assembly generated by CLC Genomics Workbench, ABySS denotes the assembly generated by ABySS with multiple k-mers and merged by running the first stage of Trans-ABySS pipeline, Velvet denotes the assembly generated by Velvet with multiple k-mers and merged by running the first stage of Trans-ABySS pipeline, and Final merged denotes the final assembly generated by combining the three sets of assembly and retain only one of longest contigs for the ones assembled by more than one assemblers.

Liu et al.

Liu et al. BMC Genomics 2012 13:595   doi:10.1186/1471-2164-13-595

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