Mapping vs Assembly

5. Mapping vs Assembly#

5.1. Mapping-first#

  • Map reads directly to a reference gene catalog or genomes.

  • Tools: Bowtie2, STAR.

5.2. Assembly-first#

  • Assemble transcripts and then annotate them.

  • Tools: metaSPAdes, MEGAHIT.

Choose based on reference availability, novelty of the community, and compute budget.

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