Dataset Information

Bambus 2: scaffolding metagenomes.

ABSTRACT:

Motivation

Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.

Results

We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly.

Availability

Bambus 2 is open source and available from http://amos.sf.net.

Contact

mpop@umiacs.umd.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Koren S

PROVIDER: S-EPMC3198580 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Bambus 2: scaffolding metagenomes.

Koren Sergey S Treangen Todd J TJ Pop Mihai M

Bioinformatics (Oxford, England) 20110916 21

<h4>Motivation</h4>Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources.<h4>Results</h4>We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing m ...[more]

PMID: 21926123

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Dataset Information

Bambus 2: scaffolding metagenomes.

Motivation

Results

Availability

Contact

Supplementary information

Publications

Bambus 2: scaffolding metagenomes.

Similar Datasets

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