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De novo assembler principles

De novo assembler principles. General principles in assembly. Dominguez Del Angel. et al. 2018. General principles in assembly. Sequence assembly Reference guided. De novo. General principles in assembly. Sequence assembly Reference guided. De novo. Reference guided assembly.

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De novo assembler principles

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  1. De novoassembler principles

  2. General principles in assembly Dominguez Del Angel. et al. 2018

  3. General principles in assembly • Sequence assembly • Reference guided • De novo

  4. General principles in assembly • Sequence assembly • Reference guided • De novo

  5. Reference guided assembly • Simple organisms • Align • Call variants • Make consensus • Complex organisms • Align and call blocks • De novo assemble left-overs • Assemble contigs Ronholm et al. 2016 Schneeberger et al. 2011

  6. De novo assembly Overlap Correction (optional) Simplification Consensus Path finding

  7. De novo assembly • De novo assemblers - correction (optional)

  8. De novo assembly • De novo assemblers - overlap Seeds K-mers e.g. de Bruijn graph e.g. mhap

  9. De novo assembly • De novo assemblers - simplification Flicek & Birney. 2009.

  10. De novo assembly • De novo assemblers - simplification Flicek & Birney. 2009.

  11. De novo assembly • De novo assemblers - path finding a - x - c - x - d - x - d a - x - b - x - c - x - d

  12. De novo assembly Wick et al. 2017 • De novo assemblers - path finding

  13. De novo assembly • De novo assemblers - consensus GTTACTTAT TGATTGACGTGA TGACTTAT TGACTTATGTTACTTATTGATTGACGTGA TGATTGACGTGA GTTACTTAT TGACTTAT TGATTGACGTGA TGACTTATGTTACTTAT TGATTGACGTGA TGATTGACGTGA

  14. De novo assembly Additional steps Scaffolds Contigs Gap filling Polishing Corrections

  15. De novo assembly • Scaffolding 10X Genomics NNNNN Mate Pair Hi - C

  16. De novo assembly • Gap filling PacBio ONT 10X Genomics NNNNNNNNNNN Assemblies: Assembly reconciliation

  17. De novo assembly • Corrections: e.g. bacterial assembly • Circular assemblies have an overlap at the end • Find conventional start site • e.g. between the genes `rpmH` and `dnaA`. • Merge the assembly again at the overlap.

  18. De novo assembly • Polishing • Multiple rounds of polishing: • Long read x2 • Short read x1

  19. De novo assembly - summary Correction Scaffolding Overlap Gap filling Simplification Correction Path finding Polishing Consensus

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