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Fig. 4 | BMC Genomics

Fig. 4

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

Fig. 4

Demonstrated assembly approaches. a All-in-one assembly using either Trinity or SOAPdenovo-trans resulted in Assembly 9 and Assembly 10, respectively). Assemblies employing multiple k-mer lengths based on SOAPdenovo-trans were merged by the same procedure as that of merging individual assemblies for the assembly and clustering approach below. b Assembly following in silico normalization of short reads with the normalization function implemented in Trinity and khmer resulted in Assembly 11 and Assembly 12. c Clustering following assembly was performed with both cd-hit-est and gicl (Assembly 13). See TableĀ 2 for statistics of the generated assemblies and Methods for the details of these three individual procedures

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