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Fig. 4 | Algorithms for Molecular Biology

Fig. 4

From: Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

Fig. 4

A theoretical scenario showing some problems repeats cause to assemblers. On the top of the figure, we can see two real transcripts containing each one a member of a repeat R. When building the assembly graph, the two copies of R may collapse into a single region of the graph, and connect the unique regions of both transcripts. The only correct assemblies are ARB and CRD, but the assembly graph also allows for the generation of the chimeric transcripts ARD and CRB, or truncated transcripts, in case the assembler chooses to be conservative

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