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Table 2 Summary of the key findings shown for each assembler

From: Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species

  Diploid species Tetraploid species
  SO TL TR SO TL TR
Number of M transcripts 0.13 (0.09) 0.13 (0.08) 0.21 (0.15) 0.20 (0.14) 0.25 (0.16) 0.46 (0.36)
Proportion of transcripts < 300 bp 0.40 (0.20) 0.24 (0.20) 0.37 (0.25) 0.38 (0.18) 0.14 (0.10) 0.32 (0.20)
Proportion of good mappings 0.68 (0.05) 0.88 (0.08) 0.82 (0.10) 0.57 (0.16) 0.90 (0.07) 0.77 (0.12)
Proportion of bases uncovered 0.02 (0.01) 0.06 (0.01) 0.05 (0.01) 0.02 (0.01) 0.13 (0.01) 0.06 (0.02)
Complete BUSCOs 1,266 (667) 1,699 (381) 1,615 (410) 1,133 (714) 1,916 (315) 1,705 (340)
Fragmented BUSCOs 328 (177) 188 (140) 240 (156) 419 (238) 132 (129) 276 (145)
Reference coverage (proteins) excl. Vaccinium 0.35 (0.03) 0.42 (0.03) 0.45 (0.01) 0.34 (0.00) 0.50 (0.10) 0.51 (0.09)
Reference coverage of A. thaliana cDNA 0.18 0.21 0.25 0.18 0.38 0.25
Proportion of representative transcripts (cd-hit-est 95% sequence identity) 0.97 (0.02) 0.81 (0.04) 0.86 (0.02) 0.97 (0.03) 0.63 (0.04) 0.80 (0.10)
Proportion of representative transcripts (cd-hit-est strict*) 1.00 (0.00) 0.92 (0.00) 0.96 (0.01) 1.00 (0.00) 0.84 (0.01) 0.94 (0.01)
  1. Mean (SD) values of all investigated diploid species (A. platanoides, V. arboreum and A. thaliana 2×) and all tetraploid species (A. pseudoplatanus, V. corymbosum and A. thaliana 4×) were calculated for SOAPdenovo-Trans (SO), TransLiG (TL) and Trinity (TR) assemblies. Bold values highlight the best performing assembler for each parameter and within each ploidy class
  2. *Transcripts are clustered with cd-hit-est with 95% sequence identity (-c), 95% length difference cutoff (-S) and 95% alignment coverage (-aS)
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