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Table 2 Summary of assemblies generated using various de novo assemblers

From: Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

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

  1. *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.