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Whole genome amplification and de novo assembly of single bacterial cells.

PloS one | 2009

Single-cell genome sequencing has the potential to allow the in-depth exploration of the vast genetic diversity found in uncultured microbes. We used the marine cyanobacterium Prochlorococcus as a model system for addressing important challenges facing high-throughput whole genome amplification (WGA) and complete genome sequencing of individual cells.

Pubmed ID: 19724646 RIS Download

Research resources used in this publication

None found

Antibodies used in this publication

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Associated grants

  • Agency: NIAID NIH HHS, United States
    Id: HHSN266200400001C

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Gordon and Betty Moore Foundation (tool)

RRID:SCR_006081

The Foundation is dedicated to advancing environmental conservation, scientific research, and patient care, as well as helping to improve quality of life in the San Francisco Bay Area--Gordon and Betty Moore''s home for more than 70 years. The Foundation is devoted to the inspirational vision articulated by our founders: creating positive outcomes for future generations. This vision guides our mission: to achieve significant, lasting and measurable results in environmental conservation, science, patient care, and the San Francisco Bay Area. A set of core valuesimpact, integrity, disciplined approach, and collaborationdirects our work. The Foundation carries out its work through the following frameworks: * Programs. The enduring management unit designed to achieve transformational change in a selected field of interest through a portfolio of integrated interventions. * Initiatives. Initiatives are built around well-developed strategies for concentrated investments, focused on the long-term and achieving significant impact. Initiatives are characterized by a portfolio approach to grantmaking, and other engagements of the Foundation, to pursue ambitious, large-scale outcomes. * Program grants. The Foundation devotes some of its grantmaking to experimentation, focused innovation, and agile response to time-sensitive, high-impact opportunities in its areas of focus. Across all initiatives and program grants, the Foundation''s grantees and partners seek to make positive changes in the world. The Foundation''s headquarters are in Palo Alto, in a building renovated with an emphasis on the environment and sustainability.

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National Science Foundation (tool)

RRID:SCR_012938

An independent federal agency created by Congress to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense They are the funding source for approximately 20 percent of all federally supported basic research conducted by America''s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing. NSF leadership has two major components: a director who oversees NSF staff and management responsible for program creation and administration, merit review, planning, budget and day-to-day operations; and a 24-member National Science Board (NSB) of eminent individuals that meets six times a year to establish the overall policies of the foundation.The director and all Board members serve six year terms. Each of them, as well as the NSF deputy director, is appointed by the President of the United States and confirmed by the U.S. Senate. At present, NSF has a total workforce of about 2,100 at its Arlington, Va., headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General. NSF is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. They are tasked with keeping the United States at the leading edge of discovery in areas from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports high-risk, high pay-off ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, they ensure that research is fully integrated with education so that today''s revolutionary work will also be training tomorrow''s top scientists and engineers NSF''s task of identifying and funding work at the frontiers of science and engineering is not a top-down process.

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Natural Sciences and Engineering Research Council of Canada (tool)

RRID:SCR_013327

NSERC aims to make Canada a country of discoverers and innovators for the benefit of all Canadians. The agency supports university students in their advanced studies, promotes and supports discovery research, and fosters innovation by encouraging Canadian companies to participate and invest in postsecondary research projects. NSERC researchers are on the vanguard of science, building on Canada''s long tradition of scientific excellence.

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Consed (tool)

RRID:SCR_005650

A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

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Velvet (tool)

RRID:SCR_010755

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux.

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