50 lines
1.4 KiB
Org Mode
50 lines
1.4 KiB
Org Mode
* locigenesis
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locigenesis is a tool that generates an immune repertoire and runs it through a sequence reader simulation tool, to generate sequencing errors.
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** Installation
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This project uses [[https://nixos.org/][Nix]] to ensure reproducible builds.
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1. Install Nix (compatible with MacOS, Linux and [[https://docs.microsoft.com/en-us/windows/wsl/about][WSL]]):
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#+begin_src shell
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curl -L https://nixos.org/nix/install | sh
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#+end_src
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1. Clone the repository:
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#+begin_src shell
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git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
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#+end_src
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3. Change the working directory to the project:
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#+begin_src shell
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cd locigenesis
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#+end_src
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4. Enter the nix-shell:
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#+begin_src shell
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nix-shell
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#+end_src
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After running these commands, you will find yourself in a shell that contains all the needed dependencies.
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** Usage
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An execution script that accepts 2 parameters is provided, the following command invokes it:
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#+begin_src shell
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./generation.sh <number of sequences> <number of reads>
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#+end_src
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- <number of sequences>: an integer that specifies the number of different sequences to generate
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- <number of reads>: an integer that specifies the number of reads to perform on each sequence
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The script will generate 2 files under the data directory:
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| HVR.fastq | Contains the original CDR3 sequence |
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| CuReSim-HVR.fastq | Contains CDR3 after the read simulation, with sequencing errors |
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