1. A Fast Hybrid Short Read Fragment Assembly Algorithm

2. Introduction Second-generation DNA technologies
Traditional : Sanger shotgun techniques
New techniques(2007 & 2008):
SSAKE, UCAKE and SHARCGS --based on greedy extension
Edena, Velvet, Euler-SR --based on graph

3. Taipan Method: Two steps
1. Greedy Extension
iteratively extended by one base at a time both in 3’ direction and 5’ direction
2. Graph-based Method
to assembly the constructed contig from previous step.

4. Example Usage: Result:
taipan -f {inputfilename} -k {minimal_overlap} [-t {threshold}] [-o {seed_occ}] [-v {verbose}] [-c {min_contig_length}]
Result:

5. Optimal spliced alignments of short sequence reads
Fabio De Bona
Bioinfromatics, 2008

6. Genome VS Transcriptome
Analysis sequence reads from genomic DNA
Sequence assemble
Align them to the genome
Transcriptome analysis
First align the single reads to the genome
Then merges the alignments to infer gene structures.

7. Genome VS Transcriptome
Reconstruct the whole genome from cDNA data
Reconstruct the transcriptome from EST data (transcripted cDNA)
DNA

8. Problem Formulation Limitation:
DNA
Limitation:
1 read length of the NG is relatively small.
2 read error rate(assuming 5%)

9. General Description Smith-Waterman Quality Score Slicing Site Info
Intron Length

10. Method 3. With Slicing Info 1. Original 2. With Quality Score
4. With Intron

11. Test Data 10 000 sequences with known alignments
three different scorings
quality information
splice site predictions
intron length