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Table 2 Transcriptome assembly statistics

From: Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Assembly No. Individuala or integratedb assembly Assembly approach Number of fragments (×106) c Raw assembly Assembly filtered by mapping count (≥5) N50 length (bp)
Number of contigs Number of subcomponents Number of contigs Number of subcomponents
1 A Trinity 22.719 222178 168924 106323 62636 3091
2 B 21.224 228165 159338 94371 45267 3634
3 C 3.569 104985 83417 37504 22331 3093
4 D 23.712 417291 291424 204328 104294 3693
5 E 16.037 383737 246347 149926 56669 4149
6 F 75.929 798982 562528 358433 182611 3956
7 G 82.453 787608 541906 375297 191055 3860
8 H 81.033 525154 348570 250433 115476 4090
9 Integrated All-in-one by Trinity 326.676 1214573 852257 653132 387456 2680
10 All-in-one by SOAPdenovo-trans, multiple k-mer lengths 326.676 1087900 745363 748019 422329 4854
11 Assembly following Trinity’s normalization 39.593d 1465425 721986 972512 330937 3755
12 Assembly after khmer 33.251d 1464412 741241 945799 314023 2898
13 Assembly and clustering 326.676 1562282 939252 996336 457323 3897
  1. aCorresponding library symbols (see Table 1) are included for individual assemblies
  2. bIntegration of all the individual assemblies
  3. cNumber of fragments for which both of the pairs passed quality control
  4. dNote that this is a number of fragments after in silico normalization