Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

Author:

Beitel Christopher W.1,Froenicke Lutz1,Lang Jenna M.1,Korf Ian F.12,Michelmore Richard W.123,Eisen Jonathan A.145,Darling Aaron E.6

Affiliation:

1. The University of California, Davis Genome Center, Davis, CA, USA

2. Department of Molecular and Cellular Biology, University of California, Davis, CA, USA

3. Department of Plant Sciences, University of California, Davis, CA, USA

4. Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA

5. Department of Evolution and Ecology, University of California, Davis, CA, USA

6. ithree institute, University of Technology Sydney, Sydney, NSW, Australia

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference28 articles.

1. Grinder: a versatile amplicon and shotgun sequence simulator;Angly;Nucleic Acids Research,2012

2. Gephi: an open source software for exploring and manipulating networks;Bastian,2009

3. The future is now: single-cell genomics of bacteria and archaea;Blainey;FEMS Microbiology Reviews,2013

4. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions;Burton;Nature Biotechnology,2013

5. ProgressiveMauve: multiple genome alignment with gene gain, loss and rearrangement;Darling;PLoS ONE,2010

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