SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Rapid hybrid de novo assembly of a microbial genome using only short reads: C Newsbot! Literature Watch 0 10-20-2011 12:40 AM
PubMed: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads Newsbot! Literature Watch 0 05-06-2011 12:40 AM
PubMed: Oral Bacterial Genome Sequencing Using the High-Throughput Roche Genome Seque Newsbot! Literature Watch 0 08-19-2010 07:50 AM
PubMed: De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sord Newsbot! Literature Watch 0 04-14-2010 03:01 AM
De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads Michael.James.Clark Literature Watch 1 04-09-2010 01:16 PM

Reply
 
Thread Tools
Old 03-12-2008, 02:12 AM   #1
b_seite
Junior Member
 
Location: germany

Join Date: Mar 2008
Posts: 1
Default Genome Res De novo bacterial genome sequencing: millions of very short reads assembly

David Hernandez, Patrice Francois, Laurent Farinelli, Magne Osteras and Jacques Schrenzel

Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals, CH-1211 Geneva 4, and 2 Fasteris SA, P.O. box 28, CH-1228 Plan-les-Ouates, Switzerland.

Novel high-throughput DNA sequencing technologies allow researchers to characterize a bacterial genome during a single experiment and at a moderate cost. However, the increase in sequencing throughput that is allowed by using such platforms is obtained at the expense of individual sequence read length, which must be assembled into longer contigs to be exploitable. This study focuses on the Illumina sequencing platform that produces millions of very short sequences that are 35 bases in length.

We propose a de novo assembler software that is dedicated to process such data. Based on a classical overlap graph representation and on the detection of potentially spurious reads, our software generates a set of accurate contigs of several kilobases that cover most of the bacterial genome. The assembly results were validated by comparing datasets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published genomes acquired by conventional sequencing of 1.5–3.0 kb fragments. We also provide indications that the broad coverage achieved by high throughput sequencing might allow for the detection of clonal polymorphisms in the set of DNA molecules being sequenced.
b_seite is offline   Reply With Quote
Old 10-05-2017, 12:26 AM   #2
tanu saroha
Junior Member
 
Location: hyderabad

Join Date: Oct 2017
Posts: 1
Default

hiiii
how do i assemble the scaffold data file to get complete bacterial (E.coli)genome sequence?the scaffold file is generated by assembling contigs and contigs are generated by assembling reads which i got from from illumina hiseq 2000 sequencer.
tanu saroha is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:26 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO