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Table 1 Spearman’s rank correlation coefficient of the scores assigned by several alternative transcriptome assembly evaluation measures to the reference-based scores from REF-EVAL

From: Evaluation of de novo transcriptome assemblies from RNA-Seq data

  KC score Contig F1 Nucleotide F1
RSEM-EVAL score 0.99 0.83 0.46
Genovo score 0.96 0.80 0.53
ALE score 0.64 0.45 0.62
N50 0.22 0.33 −0.31
Number of nucleotides 0.13 0.29 −0.21
in assembly    
Number of unique proteins 0.68 0.81 0.73
matched    
Average ortholog hit ratio 0.31 0.31 −0.19
  1. The alternative measures are defined in the main text. The evaluated assemblies were produced by Trinity, Oases, SOAPdenovo-Trans and Trans-ABySS, based on the subset of reads in the real (strand non-specific) mouse data that align to genes on chromosome 1. This subset was used in the interest of computational efficiency of the alternative measures. KC score, k-mer compression score.