70 lines
1.9 KiB
Markdown
70 lines
1.9 KiB
Markdown
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# locigenesis
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locigenesis is a tool that generates a human T-cell receptor (TCR), runs
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it through a sequence reader simulation tool and extracts CDR3.
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The goal of this project is to generate both HVR sequences with and
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without sequencing errors, in order to create datasets for a Machine
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Learning algorithm.
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## Technologies
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- [immuneSIM](https://github.com/GreiffLab/immuneSIM/): in silico
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generation of human and mouse BCR and TCR repertoires
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- [CuReSim](http://www.pegase-biosciences.com/curesim-a-customized-read-simulator/):
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read simulator that mimics Ion Torrent sequencing
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## Installation
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This project uses [Nix](https://nixos.org/) to ensure reproducible
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builds.
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1. Install Nix (compatible with MacOS, Linux and
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[WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
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``` {.shell}
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curl -L https://nixos.org/nix/install | sh
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```
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1. Clone the repository:
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``` {.shell}
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git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
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```
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1. Change the working directory to the project:
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``` {.shell}
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cd locigenesis
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```
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1. Enter the nix-shell:
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``` {.shell}
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nix-shell
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```
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After running these commands, you will find yourself in a shell that
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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
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command invokes it:
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``` {.shell}
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./generation.sh <number of sequences> <number of reads>
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```
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- \<number of sequences\>: an integer that specifies the number of
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different sequences to generate
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- \<number of reads\>: an integer that specifies the number of reads
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to perform on each sequence
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The script will generate 2 files under the data directory:
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------------------- -----------------------------------------------------------------
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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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------------------- -----------------------------------------------------------------
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