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Table 5 Comparisons of large Drosophila melanogaster 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 92193 1272 27258 6926 72.1% 81426 (88.3%) 186 (0.2%) 16 GB
50 65273 1422 26671 6832 81.8% 58101 (89.0%) 90 (0.1%) 16 GB
kCombine(SOAPdenovo-Trans)         
3 84307 1944 27391 12269 79.6% 77649 (92.1%) 1222 (1.4%) 4 GB
5 66098 2037 27153 11710 84.0% 61227 (92.6%) 976 (1.5%) 4 GB
Trans-ABySS         
20 99492 1581 27631 11103 75.7% 90854 (91.3%) 5118 (5.1%) 8 GB
50 62731 1980 27262 12151 86.0% 57508 (91.7%) 2786 (4.4%) 8 GB
kCombine(Trans-ABySS)         
3 119772 2628 27612 22113 79.3% 99021 (82.7%) 22638 (18.9%) 4 GB
5 80966 3009 27612 23110 84.5% 64161 (79.2%) 22012 (27.2%) 4 GB
  1. Notations are the same as in Table 2