LSA specifications


Unique identifier OMICS_19019
Name LSA
Alternative name Latent Strain Analysis
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A collection of multiple sequenced metagenomes.
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Requirements NumPy, SciPy, Gensim, GNU Parallel, Pyro4
Maintained Yes



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  • person_outline Eric Alm <>

Publication for Latent Strain Analysis

LSA institution(s)
Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
LSA funding source(s)
Supported in part by the Rasmussen Family Foundation; by the National Human Genome Research Institute, grant number U54HG003067; the Center for Environmental Health Sciences at MIT; the Fijian Ministry of Health and by the Earth Institute at Columbia University

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