A differential kmer analysis pipeline
Most next generation transcriptome sequencing projects rely on either mapping sequenced reads to a reference of the assembly of the reads themselves to produce a reference for mapping.
As an alternative approach, we have established a non-mapping method where differential expressed reads are determined by examining kmer abundance. While computationally expensive, this approach has the advantage in that it works well for metagenomic samples and can differentiate between very similar genes from the same or related organisms.
This method has been successfully applied to identify differential genes in coral RNA-Seq data. The pipeline can be downloaded from DiffKAP.
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