Tools
Tools
Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I.A., Belmonte, M.K. 
ORCID: 0000-0002-4633-9400, Lander, E.S., Nusbaum, C. and Jaffe, D.B.,
2008.
ALLPATHS: de novo assembly of whole-genome shotgun microreads.
Genome Research, 18 (5), pp. 810-820.
ISSN 1088-9051
|
Text
219550_PubSub1944_Belmonte.pdf Download (481kB) | Preview |
Abstract
New DNA sequencing technologies deliver data at dramatically lower costs but demand new analytical methods to take full advantage of the very short reads that they produce. We provide an initial, theoretical solution to the challenge of de novo assembly from whole-genome shotgun “microreads.” For 11 genomes of sizes up to 39 Mb, we generated high-quality assemblies from 80× coverage by paired 30-base simulated reads modeled after real Illumina-Solexa reads. The bacterial genomes of Campylobacter jejuni and Escherichia coli assemble optimally, yielding single perfect contigs, and larger genomes yield assemblies that are highly connected and accurate. Assemblies are presented in a graph form that retains intrinsic ambiguities such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. For both C. jejuni and E. coli, this assembly graph is a single edge encompassing the entire genome. Larger genomes produce more complicated graphs, but the vast majority of the bases in their assemblies are present in long edges that are nearly always perfect. We describe a general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads.
| Item Type: | Journal article | ||||
|---|---|---|---|---|---|
| Publication Title: | Genome Research | ||||
| Creators: | Butler, J., MacCallum, I., Kleber, M., Shlyakhter, I.A., Belmonte, M.K., Lander, E.S., Nusbaum, C. and Jaffe, D.B. | ||||
| Publisher: | Cold Spring Harbor Laboratory Press | ||||
| Place of Publication: | Cold Spring Harbor, NY | ||||
| Date: | 2008 | ||||
| Volume: | 18 | ||||
| Number: | 5 | ||||
| ISSN: | 1088-9051 | ||||
| Identifiers: |
|
||||
| Rights: | Copyright © 2008, Cold Spring Harbor Laboratory Press | ||||
| Divisions: | Schools > School of Social Sciences | ||||
| Record created by: | EPrints Services | ||||
| Date Added: | 09 Oct 2015 11:11 | ||||
| Last Modified: | 09 Jun 2017 13:52 | ||||
| URI: | https://irep.ntu.ac.uk/id/eprint/24156 |
Actions (login required)
 |
Edit View |
Views
Views per month over past year
Downloads
Downloads per month over past year
