a fast hybrid short read fragment assembly algorithm

A Fast Hybrid Short Read Fragment Assembly Algorithm

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

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.

Example• Usage:taipan -f {inputfilename} -k {minimal_overlap} [-t {threshold}] [-o {seed_occ}] [-v

{verbose}] [-c {min_contig_length}]

• Result:

Optimal spliced alignments of short sequence reads

Fabio De Bona

Bioinfromatics, 2008

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.

Genome VS Transcriptome

• Reconstruct the whole genome from cDNA data

• Reconstruct the transcriptome from EST data (transcripted cDNA)

DNA

Problem Formulation

Limitation:

1 read length of the NG is relatively small.

2 read error rate(assuming 5%)

DNA

General Description

Smith-Waterman

– Quality Score

– Slicing Site Info

– Intron Length

Method

1. Original

2. With Quality Score

3. With Slicing Info

4. With Intron

Test Data• 10 000 sequences with known alignments• three different scorings

1.quality information2.splice site predictions3. intron length