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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.