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Assembly

Assembly. Sequence assembly . Reads. Contigs. Scaffolds. Four approaches to assembly. Naïve approach Greedy approach Overlap / Layout / Consensus de Bruijn Graphs. Current assemblers. LIGR Assembler (derived from TIGR Assembler) MIRA (Mimicking Intelligent Read Assembly) Newbler

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Assembly

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  1. Assembly

  2. Sequence assembly Reads Contigs Scaffolds

  3. Four approaches to assembly • Naïve approach • Greedy approach • Overlap / Layout / Consensus • de Bruijn Graphs

  4. Current assemblers LIGR Assembler (derived from TIGR Assembler) MIRA (Mimicking Intelligent Read Assembly) Newbler Phrap SSAKE SOAPdenovo SPAdes Velvet • AMOS • CAP3 • Celera WGA Assembler • CLC Genomics Workbench • DNA Dragon • DNAnexus • Euler • Geneious • IDBA (Iterative De Bruijn graph short read Assembler) • KiKi

  5. Current assemblers LIGR Assembler (derived from TIGR Assembler) MIRA (Mimicking Intelligent Read Assembly) Newbler Phrap SSAKE SOAPdenovo SPAdes Velvet • AMOS • CAP3 • Celera WGA Assembler • CLC Genomics Workbench • DNA Dragon • DNAnexus • Euler • Geneious • IDBA (Iterative De Bruijn graph short read Assembler) • KiKi

  6. Assembly RAST • Pipeline for automatic assembly • Works with fasta, fastq, single end, paired end • Runs multiple assemblers in parallel • Combines contigs

  7. Hybrid assembly Geni Silva

  8. Sequence assembly Reads Contigs Scaffolds

  9. scaffold_builder http://edwards.sdsu.edu/scaffold_builder Silva et al. Source Code for Biology and Medicine 2013, 8:23

  10. Bandage to view graphs Bandage: Ryan Wick: http://rrwick.github.io/Bandage

  11. Bandage to view graphs Bandage: Ryan Wick: http://rrwick.github.io/Bandage

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