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Sci China Life Sci. 2011 Dec;54(12):1129-33. doi: 10.1007/s11427-011-4256-9. Epub 2012 Jan 7.

De novo transcriptome assembly of RNA-Seq reads with different strategies.

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  • 1Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai 200241, China.


De novo transcriptome assembly is an important approach in RNA-Seq data analysis and it can help us to reconstruct the transcriptome and investigate gene expression profiles without reference genome sequences. We carried out transcriptome assemblies with two RNA-Seq datasets generated from human brain and cell line, respectively. We then determined an efficient way to yield an optimal overall assembly using three different strategies. We first assembled brain and cell line transcriptome using a single k-mer length. Next we tested a range of values of k-mer length and coverage cutoff in assembling. Lastly, we combined the assembled contigs from a range of k values to generate a final assembly. By comparing these assembly results, we found that using only one k-mer value for assembly is not enough to generate good assembly results, but combining the contigs from different k-mer values could yield longer contigs and greatly improve the overall assembly.

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