Navigation

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.

Previous topic

The Opinionated Guide to Sequencing and Assembly

Next topic

Our list of good practices in (meta)genome assembly

This Page

Navigation

LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

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.

© Copyright 2013, Holly Bik, C. Titus Brown, Nick Loman, Lex Nederbragt, Jared Simpson. Created using Sphinx 1.1.3.

Edit this document!

This file can be edited directly through the Web. Anyone can update and fix errors in this document with few clicks -- no downloads needed.

  1. Go to The 10+ Commandments of Assembly on GitHub.
  2. Edit files using GitHub's text editor in your web browser (see the 'Edit' tab on the top right of the file)
  3. Fill in the Commit message text box at the bottom of the page describing why you made the changes. Press the Propose file change button next to it when done.
  4. Then click Send a pull request.
  5. Your changes are now queued for review under the project's Pull requests tab on GitHub!

For an introduction to the documentation format please see the reST primer.