Ab initio transcriptome assembly
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- Ab initio transcriptome assembly search for term
When a reference genome for the target transcriptome is available, the transcriptome assembly can be built upon it. In general, this strategy — which is known as ‘reference-based’ or ‘ab initio’ assembly — involves three steps. First, RNA-seq reads are aligned to a reference genome using a splice-aware aligner, such as Blat45, TopHat46, SpliceMap, MapSplice or GSNAP. Second, overlapping reads from each locus are clustered to build a graph representing all possible isoforms. The final step involves traversing the graph to resolve individual isoforms. Examples of methods that use the reference-based strategy include Cufflinks20, Scripture16 and others (Martin 2011)
