coolneng
/
locigenesis
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity
55 Commits 1 Branch 5 Tags 213 KiB
R 82.8%
Nix 12.6%
Shell 4.6%
Go to file
coolneng 1f7b40d224
Remove redundant JDK dependency 		2021-05-04 01:57:34 +02:00
data Add v_segments and j_segments objects 2021-04-07 18:32:58 +02:00
docs Add literate programming notebook 2021-03-23 18:24:12 +01:00
nix Initial commit 2021-02-18 00:01:17 +01:00
src Fix HVR end position computation 2021-05-03 21:51:32 +02:00
.gitignore Generate FASTQ files from the simulated repertoire 2021-04-22 13:59:45 +02:00
LICENSE.md Initial commit 2021-02-18 00:01:17 +01:00
README.org Add usage instructions to the README 2021-05-04 01:28:49 +02:00
generation.sh Add usage instructions to the README 2021-05-04 01:28:49 +02:00
shell.nix Remove redundant JDK dependency 2021-05-04 01:57:34 +02:00

README.org

locigenesis

locigenesis is a tool that generates an immune repertoire and runs it through a sequence reader simulation tool, to generate sequencing errors.

Installation

This project uses Nix to ensure reproducible builds.

  1. Install Nix (compatible with MacOS, Linux and WSL):
curl -L https://nixos.org/nix/install | sh
  1. Clone the repository:
git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
  1. Change the working directory to the project:
cd locigenesis
  1. Enter the nix-shell:
nix-shell

After running these commands, you will find yourself in a shell that contains all the needed dependencies.

Usage

An execution script that accepts 2 parameters is provided, the following command invokes it:

./generation.sh <number of sequences> <number of reads>
  • <number of sequences>: an integer that specifies the number of different sequences to generate
  • <number of reads>: an integer that specifies the number of reads to perform on each sequence

The script will generate 2 files under the data directory:

HVR.fastq Contains the original CDR3 sequence
CuReSim-HVR.fastq Contains CDR3 after the read simulation, with sequencing errors