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
c | Transcripts | n50 | Blast | Full | Spec | Unique | Transloc | Memory |
|---|---|---|---|---|---|---|---|---|
SOAPdenovo-Trans | Â | Â | Â | Â | Â | Â | Â | Â |
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) | Â | Â | Â | Â | Â | Â | Â | Â |
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 | Â | Â | Â | Â | Â | Â | Â | Â |
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) | Â | Â | Â | Â | Â | Â | Â | Â |
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 |