About Microbiome Search Engine

Database Information

Search engine: Meta-Storms 2.2.1

Database information:

Download

  • The standalone software (version std 2.2.1, lastest release: Dec. 1, 2018)
  • Linux X86_64 (bin package / src package)
  • Mac OS X (bin package / src package)
  • Here we provide a demo run with 20 human oral microbiome samples. This dataset has been integrated into the above packages.
  • System requirement
  • Mac OS X needs to install the compiler that supports OpenMP by
    brew install gcc --without-multilib
  • Quick installation
  • Type the following commands in the directory that contains the package for quick installation:
    tar -xzvf meta-storms-2-std-2.2.1.tar.gz#Extract the package
    cd meta-storms-2-std#Go to the package directory
    source install.sh#Automatic installation
  • The example dataset could be found at “example” folder. Check the “example/Readme” for details about the demo run.
  • The sequence profiling software
  • We strongly recommend to use Parallel-META 3 for sequence profiling.
  • Supplementary
  • The test code and datasets for reproducing the results of manuscript "Model-free disease classification across cohorts via microbiome search" is available here (Linux X86_64 / Mac OS X, ~ 892 MB). See “Readme.txt” in the package for usage and details.

Citation

    1. X. Su*, G. Jing, D. McDonald, H. Wang, Z. Wang, A. Gonzalez, Z. Sun, S. Huang, J. Navas, R. Knight* and J. Xu*. Identifying and predicting novelty in microbiome studies, mBio, 2018. Link
    2. X.Su1, X. Wang1, G. Jing and K. Ning*. GPU-Meta-Storms: Computing the structure similarities among massive amount of microbial community samples using GPU, Bioinformatics, 2014. Link
    3. X. Su, J. Xu and K. Ning*. Meta-Storms: Efficient Search for Similar Microbial Communities Based on a Novel Indexing Scheme and Similarity Score for Metagenomic Data, Bioinformatics, 2012. Link

Updates

    1. Nov. 21, 2018. The total number of samples in MSE has been updated to 177,022.
    2. Nov. 13, 2018. Our manuscript entitled “Identifying and predicting novelty in microbiome studies” is published by mBio.
    3. Oct. 26, 2018. The new search engine kernel software (Meta-Storms 2 ver. 2.2.1) is released.
    4. Oct. 9, 2018. MSE ver. 1.1 is online with MAS, MNS and MFI.

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