- Note original repository was at: https://github.com/Benjamin-Vincent-Lab/stig . Moved on 2/12/2024
STIG is a tool for creating artificial T-cell repertoires and producing simulated sequencing data from them. Many characteristics of the repertoires can be customized (e.g. alpha/beta & gamma/delta distribution; allele substitution for V, D, J, and C regions). Simulated sequencing data can be generated in DNA or RNA space, with a variety of customization options (e.g. paired vs. single-end reads, user-defined distribution of read & insert lengths). Applications include evaluating and optimizing tools for performing analysis of T-cell receptors.
- A working Python 3 installation. This has been been tested with 3.5.2.
- Two python package requirements: 'numpy' for numeric distributions required for making repertoires, and 'pyyaml' for unpacking the YAML-formatted TCR recombination data
- Reference chromosomes placed in the working directory (
data, by default). See "Reference chromosomes" below.
STIG is distributed with allele data from IMGT, as well as reference coordinates for that allele data compatible with hg38. You will need a copy of the hg38 chromosome 7 and 14 reference files, which may be found at http://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/ Look for chr7.fa.gz and chr14.fa.gz, and unpack these into your working directory (defaults to data). There's also a Makefile in the working directory included with STIG, running cd data && make fetch will fetch and unpack hg38 chromosomes 7 and 14.
No installation is required. STIG can be run directly out of its extracted package directory, once the reference chromosomes are installed in the working directory.
STIG can be called directly from its package directory. Use ./lib/stig --help to view the command-line help menu.
The latest release can be found at https://github.com/vincentlaboratories/stig
Documentation for the most recent version is available on the project website. A copy of the manual is included in each version as Markdown-formatted text.
This software is copyright (C) 2019 The University of North Carolina at Chapel Hill.
STIG is free sofware licensed under the GNU GPL version 3 or later http://gnu.org/licenses/gpl.html.
T-cell segment allele files are copyright IMGT(R), and for academic research only. Please note that some of these files have been modified for the purposes of STIG: See the manual for details.
- IMGT(R), the international ImMunoGeneTics information system(R) http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)
- Maintainer: Mark Woodcock mark.woodcock@unchealth.unc.edu
- GitHub: https://github.com/vincentlaboratories/stig