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Table 4 Comparisons of Arabidopsis thaliana transcriptome assemblies of SOAPdenovo-Trans, Trans-ABySS and kCombine with k=25 over different values of k-mer coverage cutoff c

From: A divide-and-conquer algorithm for large-scale de novo transcriptome assembly through combining small assemblies from existing algorithms

c Transcripts n50 Blast Full Spec Unique Transloc Memory
SOAPdenovo-Trans         
20 88808 841 27325 1583 78.7% 76542 (86.2%) 44 (0.0%) 4 GB
50 59638 887 24554 1302 82.9% 51402 (86.2%) 38 (0.1%) 4 GB
kCombine(SOAPdenovo-Trans)         
3 88611 1103 29057 2666 81.7% 81576 (92.1%) 1324 (1.5%) 4 GB
5 70854 1125 28020 2354 84.1% 65574 (92.5%) 972 (1.4%) 4 GB
Trans-ABySS         
20 124125 830 28414 4372 88.0% 119120 (96.0%) 1574 (1.3%) 2 GB
50 62093 1006 25533 3109 91.9% 59420 (95.7%) 1010 (1.6%) 2 GB
kCombine(Trans-ABySS)         
3 90109 1147 30333 3261 82.2% 83037 (92.2%) 4242 (4.7%) 4 GB
5 59411 1315 29266 3303 88.0% 54903 (92.4%) 3464 (5.8%) 4 GB
  1. Notations are the same as in Table 2