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 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

5. 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

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:

11. Bandage to view graphs
Bandage: Ryan Wick: