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De novo assembler principles

This guide explores principles and methods of de novo assembly in bioinformatics, covering sequence assembly, reference-guided and de novo approaches, simplification, consensus building, path finding, and polishing techniques.

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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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