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Title: Preliminary High-Throughput Metagenome Assembly

Abstract

Metagenome data sets present a qualitatively different assembly problem than traditional single-organism whole-genome shotgun (WGS) assembly. The unique aspects of such projects include the presence of a potentially large number of distinct organisms and their representation in the data set at widely different fractions. In addition, multiple closely related strains could be present, which would be difficult to assemble separately. Failure to take these issues into account can result in poor assemblies that either jumble together different strains or which fail to yield useful results. The DOE Joint Genome Institute has sequenced a number of metagenomic projects and plans to considerably increase this number in the coming year. As a result, the JGI has a need for high-throughput tools and techniques for handling metagenome projects. We present the techniques developed to handle metagenome assemblies in a high-throughput environment. This includes a streamlined assembly wrapper, based on the JGI?s in-house WGS assembler, Jazz. It also includes the selection of sensible defaults targeted for metagenome data sets, as well as quality control automation for cleaning up the raw results. While analysis is ongoing, we will discuss preliminary assessments of the quality of the assembly results (http://fames.jgi-psf.org).

Authors:
; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1170764
Report Number(s):
LBNL-6770E
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Conference
Resource Relation:
Conference: JGI 2nd Annual User's Meeting
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS; High-Throughput, Metagenome Assembly, US Sludge, Whole-Genome Shutgun

Citation Formats

Dusheyko, Serge, Furman, Craig, Pangilinan, Jasmyn, Shapiro, Harris, and Tu, Hank. Preliminary High-Throughput Metagenome Assembly. United States: N. p., 2007. Web.
Dusheyko, Serge, Furman, Craig, Pangilinan, Jasmyn, Shapiro, Harris, & Tu, Hank. Preliminary High-Throughput Metagenome Assembly. United States.
Dusheyko, Serge, Furman, Craig, Pangilinan, Jasmyn, Shapiro, Harris, and Tu, Hank. Mon . "Preliminary High-Throughput Metagenome Assembly". United States. doi:. https://www.osti.gov/servlets/purl/1170764.
@article{osti_1170764,
title = {Preliminary High-Throughput Metagenome Assembly},
author = {Dusheyko, Serge and Furman, Craig and Pangilinan, Jasmyn and Shapiro, Harris and Tu, Hank},
abstractNote = {Metagenome data sets present a qualitatively different assembly problem than traditional single-organism whole-genome shotgun (WGS) assembly. The unique aspects of such projects include the presence of a potentially large number of distinct organisms and their representation in the data set at widely different fractions. In addition, multiple closely related strains could be present, which would be difficult to assemble separately. Failure to take these issues into account can result in poor assemblies that either jumble together different strains or which fail to yield useful results. The DOE Joint Genome Institute has sequenced a number of metagenomic projects and plans to considerably increase this number in the coming year. As a result, the JGI has a need for high-throughput tools and techniques for handling metagenome projects. We present the techniques developed to handle metagenome assemblies in a high-throughput environment. This includes a streamlined assembly wrapper, based on the JGI?s in-house WGS assembler, Jazz. It also includes the selection of sensible defaults targeted for metagenome data sets, as well as quality control automation for cleaning up the raw results. While analysis is ongoing, we will discuss preliminary assessments of the quality of the assembly results (http://fames.jgi-psf.org).},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Mar 26 00:00:00 EDT 2007},
month = {Mon Mar 26 00:00:00 EDT 2007}
}

Conference:
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