Install Seq2Fun

Seq2Fun was written in C/C++11 and can be installed on Linux or Mac OS X (with Xcode and Xcode Command Line Tools installed). We have tested Seq2Fun on Ubuntu (16.04 LTS and above) and macOS Catalina.

  1. Download & compile

    Click here to check and download all Seq2Fun stable releases. The latest development version is hosted on GitHub. After download, from within the folder containing the downloaded package, issue the following commands:

    >tar -xvzf seq2fun_v1.2.5.tar.gz
    >cd Seq2fun/src/
    >make clean
    >make

    or the latest version
    >git clone https://github.com/xia-lab/Seq2Fun.git
    >cd Seq2Fun/src/
    >make clean
    >make

  2. Run a small test

    There are four sub folders under seq2fun - src, bin, database and testdata. The bin folder contains the binary code we just complied. The testdata contains a small test data from the Case Study. From within the testdata folder, issue the following commands:

    >../bin/seq2fun --sampletable sample.txt --tfmi birds_cdhit99_proteins.fmi --genemap birds_protein_ko_species_cdhit99.txt -w 8 --profiling -V --outputMappedCleanReads --outputReadsKOMap

    The progress will be displayed on the terminal. The screenshot below (from macOS Catalina v10.15.5) shows the last few lines:

    You will see many files generated in the current folder:

  3. Submit KO abundance table to our website-based tool NetworkAnalyst (optional) for comprehensive data analysis and visual exploration.

    Seq2Fun generates two KO abundance tables:
    All_sample_KO_abundance_table.txt and All_sample_KO_abundance_table_submit2networkanalyst.txt, the later will be used to submit to NetworkAnalyst.

  4. Seq2Fun release history:

    Click here to download all the versions.
    30-08-2021 - seq2fun_v1.2.5 released
    23-08-2021 - seq2fun_v1.2.4 released
    18-06-2021 - seq2fun_v1.2.3 released
    05-06-2021 - seq2fun_v1.2.2 released
    03-31-2021 - seq2fun_v1.2.1 released
    03-26-2021 - seq2fun_v1.2.0 released
    03-22-2021 - seq2fun_v1.1.4 released
    01-14-2021 - seq2fun_v1.1.2 released
    12-06-2020 - seq2fun_v1.1.0 released
    08-24-2020 - seq2fun_v1.0.0 released