The 10+ Commandments of Assembly

Nick Loman (corr), et al.

  1. Do I really need to assemble?
  2. Good data is more important than choice of assembler.
  3. Have a specific goal.
  4. An assembly is a hypothesis to be tested.
  5. Assembly programs are not haplotype aware.
  6. More data may help.
  7. If you haven’t found contamination in your data you haven’t looked hard enough.
  8. A different assembler may help.
  9. Make sure the assembly agrees with the reads that were used to put it together.
  10. N50 is not a measure of quality.
  11. But we don’t have a measure of quality.
  12. Avoid: Wheat, Fish, and Soil.
  13. Trust contigs more than scaffolds more than gap filling.
  14. The answer to your question may not be in your data.
  15. A bad assembly that completes, is better than a good assembly that doesn’t.

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Development and posting of this material, and the associated workshop, were supported by Grant Number R25HG006243 from the National Human Genome Research Institute and an NSF OCI supplement to NSF DBI-0939454.

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