yasim_sctcr -- Yet Another SIMulator for Single-Cell T-Cell Receptor Sequencing (scTCR-Seq)

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Introduction

Single-Cel T-Cell Receptor (TCR) Sequencing (scTCR-Seq) is an important method in studying the diversity and dynamics of T-cell populations in organisms. However, since the number of publicly available scTCR-Seq datasets is limited, researchers often need to reconstruct TCR contigs from scRNA-Seq data, and a benchmark of such tools is required.

This software provides an easy way to simulate Next-Generation Sequencing (NGS)-based scTCR-Seq using Illumina sequencer simulator. With realistic TCR contig constructed from statistics of 1.08 million human TCR V/J CDR3 sequences from hUARdb, it supports simulation of TCR contigs from arbitrary cell number, sequencing depth, read length with Paired/Single End support. It also supports mixing scTCR-Seq data with simulated scRNA-Seq data, which allows calculation of both precision and sensitivity.

Installation

Using the Pre-Built Version from PYPI

You need a working Python interpreter (CPython implementation) >= 3.8 (recommended 3.9) and the latest pip to install this software from PYPI. Command:

pip install yasim-sctcr==1.0.0

You are recommended to use this application inside a virtual environment like venv, virtualenv, pipenv, conda, or poetry.

Build from Source

Before building from the source, get a copy of the latest source code from https://github.com/WanluLiuLab/yasim-sctcr using Git:

git clone https://github.com/WanluLiuLab/yasim-sctcr

Or, if you prefer to use GNU Wget.

wget -o yasim-master.zip https://github.com/WanluLiuLab/yasim-sctcr/archive/refs/heads/master.zip
unzip yasim-master.zip

You need Python interpreter (CPython implementation) >= 3.8, latest PYPA build, and setuptools to build this software. You are recommended to build the software in a virtual environment provided by virtualenv, etc.

Build and install the simulator using:

cd yasim-sctcr
python3 -m build
pip install dist/yasim-sctcr-1.0.0-py3-none-any.whl

Apart from the above instructions, you should also install ART which is a general-purpose NGS DNA-Seq simulator and is available from Conda and APT. Tested versions are 2.5.8 (June 6, 2016).

News

The initial release version is 0.1.0 at 2023/08/06.

• 1.0.0 (2024/06/12): Addressed several problems proposed by the reviewers:
  • Simulation for TRC gene added to generate_tcr_cache and rearrange_tcr.
  • Support the simulation of non-productive TCRs on a fixed ratio.
  • The scRNA-Seq simulator accepts outputs from other scNRA-Seq simulators.
  • Supported the distribution of TCR repertoire created by clonal expansion.
  • scTCR-Seq-specific fragment length and bias.
  • Supported V/J usage bias.