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.

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