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ALLPATHS-LG

Provides a whole‐genome shotgun assembler that can generate high‐quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. The ALLPATHS-LG assemblies are not necessarily linear, but instead are presented in the form of a graph. This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies. ALLPATHS‐LG requires high sequence coverage of the genome in order to compensate for the shortness of the reads. The precise coverage required depends on the length and quality of the paired reads, but typically is of the order 100x or above.

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ALLPATHS-LG classification

ALLPATHS-LG specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

ALLPATHS-LG distribution

versioning

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No versioning.

ALLPATHS-LG support

Documentation

Maintainer

  • Eric Lander <>

Additional information

http://software.broadinstitute.org/allpaths-lg/blog/?page_id=2

Credits

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Publications

Institution(s)

Broad Institute of MIT and, Harvard, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA

Funding source(s)

This work was carried out with the aid of federal funds provided by the National Institutes of Health, Department of Health and Human Services, via Grants U54HG003067 and R01HG003474 through the National Human Genome Research Institute and Contract HHSN2722009000018C through the National Institute of Allergy and Infectious Diseases.

Link to literature

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