Assembly.

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Presentation transcript:

Assembly

Sequence assembly Reads Contigs Scaffolds

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

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

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

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

Hybrid assembly Geni Silva

Sequence assembly Reads Contigs Scaffolds

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

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

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