VELVET- Using de Bruijn graphs for the de novo sequence assembly of very short reads

Dec 03, 2012

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Velvet: de novo short read assembly - Edinburgh NextGenBUG. 08/05/2007. Slide 2. Presentation overview. De Bruijn graphsResultsScaling up to mammalian genomesOutlook. De Bruijn graphs. . Velvet: de novo short read assembly - Edinburgh NextGenBUG. 08/05/2007. Slide 4. A quick example. TAGTCGAGGCTT

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VELVET- Using de Bruijn graphs for the de novo sequence assembly of very short reads

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De Novo Genome Assembly Using vSMP

De Novo Genome Assembly Using vSMP. Wayne Pfeiffer (SDSC/UCSD) August 10, 2011. Goal: determine the DNA sequence of the chromosomes that make up a genome. Background Chromosomes consist of two long DNA molecules in a double helix

479 views • 18 slides

Parallel de novo Assembly of Large Genomes from Paired Short Reads

Parallel de novo Assembly of Large Genomes from Paired Short Reads. Srinivas Aluru Electrical and Computer Engineering Iowa State University Computer Science and Engineering Indian Institute of Technology Bombay. Sequencing Technology (1977-2005). Sanger Sequencing 500-1000 bp per run

459 views • 32 slides

De novo assembly from Illumina

350 views • 14 slides

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. David Hernandez, Patrice François, Laurent Farinelli, Magne Østerås, Jacques Schrenzel. Presented by Lucas Lochovsky. Outline. Introduction Edena’s Methodology Reducing Read Redundancy

757 views • 48 slides

Hybrid error correction and de novo assembly of single-molecule sequencing reads

Hybrid error correction and de novo assembly of single-molecule sequencing reads. Presented by George Roberts III.

930 views • 64 slides

Genovo : De Novo Assembly for Metagenomes

Genovo : De Novo Assembly for Metagenomes. Gao Song 2010/07/14. Outline. Overview of Metagenomices Current Assemblers Genovo Assembly. Overview of Metagemices. Motivation. Metagenomics is: Why Do We Need Metagenomics ? Snapshot of bacterial community Cannot be cultivated. <1%.

407 views • 22 slides

Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads

Harry Presman. Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads. Overview. Motivation Assembly Results Advantages/Limitations. Motivation. Next-gen sequencers produce short read-lengths Useful for polymorphism discovery Difficult to assemble whole genomes

311 views • 16 slides

PE-Assembler: De novo assembler using short paired-end reads

PE-Assembler: De novo assembler using short paired-end reads. Pramila Nuwantha Ariyaratne. Outline. Method Read screening Seed building Contig extension Scaffolding Gap filling Result. Data-sets Used. Single end reads Paired end reads ReadLength ( from 25bp to 100bp)

355 views • 21 slides

De Novo Sequencing and Homology Searching with De Novo Sequence Tags

De Novo Sequencing and Homology Searching with De Novo Sequence Tags. Inexact protein DB. protein DB. Possible Ways to Interpret MS/MS Data. MS/MS Spectra. 2. de novo sequencing. peptides. homology search. database search. 1. 3. peptides. h omologous peptides. Why Bother?.

691 views • 50 slides

Assembling and comparing genomes or transcriptomes using de Bruijn graphs

Assembling and comparing genomes or transcriptomes using de Bruijn graphs. Daniel Zerbino, Marcel Schulz, Wendy Lee, Ewan Birney and David Haussler. Outline. De Bruijn graphs Construction and error correction Repeat resolution Resolving repeats using long reads or paired-end reads

651 views • 49 slides

De novo assembly of RNA

De novo assembly of RNA. Steve Kelly www.stevekelly.eu Slides are available at: http://bioinformatics.plants.ox.ac.uk/EBI_2014/EBI_2014.ppt Example data is available at: http://bioinformatics.plants.ox.ac.uk/EBI_2014/reads.zip. What is a de novo transcriptome?.

600 views • 43 slides

De-novo Assembly

De-novo Assembly. Day 4. The Challenge. Given many (millions or billions) of reads, produce a linear (or perhaps circular) genome Issues : Coverage Errors in reads Reads vary from very short (35bp) to quite long (800bp), and are double-stranded Non-uniqueness of solution

606 views • 19 slides

De Novo Repeat Classification and Fragment Assembly

De Novo Repeat Classification and Fragment Assembly. 석사 1 년 김 우 연. PROGRAMS related Repeat. Repeat Annotation - libraries RepeatMasker ( A.F.A. Smit and P. Green, unpubl. ) MaskerAid ( Bedell et al. 2000 ) No de novo compilation Repeat Analysis RepeatMatch ( Delcher et al. 1999 )

417 views • 20 slides

De novo assembly from clinical sample

De novo assembly from clinical sample. Anna Shcherbina Bioinformatics Challenge Day 01/10/2013. This work is sponsored by the Defense Threat Reduction Agency under Air Force Contract #FA8721-05-C-0002.

231 views • 11 slides

Assembly of Solexa tomato reads

Assembly of Solexa tomato reads. Mar í a Jos é Truco Bioinformatics and Genomics Program CRG-Centre de Regulació Gen ò mica Barcelona. RESULTS : Testing of the three tomato run concentrations. Methodology: -Mixture of 9 BACs (2 incomplete). Three concentration runs: 1 pM , 2pM and 4 pM

163 views • 5 slides

De novo genome assembly

De novo genome assembly. Andrew Tritt September 13, 2012. Outline. Background Graphs Genome assembly Old  Assembly in the Sanger days Overlap-layout-consensus New  Assembly in the era of big data De Bruijn graphs Scaffolding  utilizing paired-end data Hands On

987 views • 24 slides

De Bruijn Sequences

De Bruijn Sequences. Define an alphabet A consisting of k elements E.g. A={0,1} , A={ a,b,c }, A= { 图，论，很，好，玩 } K=2 ， K=3 ， and K=5 in the preceding example. Consider the possible subsequences of length n that can be created using the defined alphabet E.g. Let n=2 A={0,1}

482 views • 12 slides

Human Chromosome Y Sequence Assembly using Oxford Nanopore Reads

First Human chromosome Y sequence was published nearly two decades ago, yet the full chr Y sequence is not competently resolved due to high repeat content. Chromosome Y is a highly complex and possess great challenges in generating a high quality full length assembly.

103 views • 2 slides

De Novo Genome Assembly - Introduction

De Novo Genome Assembly - Introduction. Henrik Lantz - NBIS/ SciLife /Uppsala University. De Novo Assembly - Scope. De novo genome assembly - not reference based Bioinformatics course - not biological interpretation Practical experience - focus on computer exercises

532 views • 48 slides

De Novo Genome Assembly - Introduction

De Novo Genome Assembly - Introduction. Henrik Lantz - BILS/ SciLife /Uppsala University. De Novo Assembly - Scope. De novo genome assembly of eukaryote genomes Bioinformatics in general, programs in particular Practical experience Ease of entry - not memorization.

409 views • 29 slides

De novo assembly validation

De novo assembly validation. Tools and techniques to evaluate de novo assemblies in the NGS era. Martin Norling. Why do we need assembly validation?. Is my assembly correct? I used all the assemblers – now, which result should I use? Is this assembly good enough for annotation?.

221 views • 19 slides

De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer

493 views • 48 slides

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