neofind

Discover and analyze neoantigens using RNA, Ribo, and WES/WGS sequence data.

• neofind
• Overview
• Requirements
• neofind modules
  • neofind gene
  • Usage
• Docker
• Conda Environment
• Cite neofind

Overview

neofind is a pipeline for discovering and analyzing neoantigens using RNA, Ribo, and WES/WGS sequence data.

It is recommended to use the docker or conda environment to run the pipeline.

Requirements

1. Python 3.10+
2. Python modules:
   • pandas
   • numpy
   • scipy
   • sklearn
   • matplotlib
   • seaborn
   • pysam
3. minimap2
4. samtools
5. bedtools

neofind modules

The main module of neofind, which includes the following sub-modules:

• gene
• count

neofind gene

Usage

neofind gene -i ../input/{}/pass.fq.gz -r ../reference/fasta/genome.fa -o ./{}_gene.sam --parms '--secondary=no --cs -a --sam-hit-only'

neofind netmhcpan-extract
-i output_NetMHCpan.xls
-f binders.fasta
--input-fasta input_predict_neoantigen.fasta
--output-bed binders.bed
--rank-type BA_Rank

Docker

If the user has docker installed, the following command can be used to run the pipeline in a docker container:

docker run -v /path/to/data:/data -it neofind/neofind:latest /bin/bash

Conda Environment

If the user has conda installed, the following command can be used to create a conda environment for neofind:

1. Install conda
2. Create a new conda environment: conda create -n neofind python=3.12
3. Activate the environment: conda activate neofind
4. Install the required packages: conda install -c bioconda minimap2 samtools bedtools
5. Install the required python packages: pip install pandas numpy scipy sklearn matplotlib seaborn pysam
6. Clone the neofind repository: git clone https://github.com/LegendZDY/neofind.git

Cite neofind

If you use neofind in your research, please cite the following paper: