T-IDBA

T-IDBA is an iterative De Bruijn Graph De Novo short read assembler for transcriptome. It is purely de novo assembler based on only RNA sequencing reads. In this assembler, not only the reads but also the pair-end information is used to increase the k value in the accumulated de Bruijn graph. Because of the nature of the transcriptome, the transcripts from different genes share only very few repeat patterns. Hence, de Bruijn graph will be decomposed into small connected components when k is large enough. Each component corresponds to one gene in most cases and contains not many transcripts. A heuristic algorithm based on pair-end reads is then used to find the isoforms in T-IDBA.

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References in zbMATH (referenced in 1 article )

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  1. Nimmy, Sonia Farhana; Kamal, M.S.: Next generation sequencing under de novo genome assembly (2015)