guobioinfolab/catt repository overview

⁠CATT

CATT: an ultra-sensitive and accurate tool for characterizing T cell CDR3 sequences in bulk and single cell TCR-Seq and RNA-Seq data. The tool can be found in:

• HomePage: http://bioinfo.life.hust.edu.cn/CATT⁠

• Github: https://github.com/GuoBioinfoLab/CATT⁠

⁠Overview

CATT(CharActerzing TCR repertoires) is a tool for detecting CDR3 sequences from any TCR containing raw sequencing data (including TCR-seq, RNA-seq and scRNA-seq, etc...).

The tool has the following feature:

• Easy to use: CATT employs a totally data-driven algorithm, which is self-adaption to input data without any additional parameters.
• Precisely and efficiently extract T cell CDR3 sequences from most types of TCR containing raw sequencing data. Based on specially designed assembly, CATT could recover more CDR3 sequences than other tools even from short reads.

⁠Installation/Download

⁠Using Docker

Docker is a computer program that performs operating-system-level virualization. Using docker, users could easily install catt and run catt in virtual enviroment.

1. Download and install Docker, Docker Homepage⁠

2. Download latest stable CATT docker image

docker pull guobioinfolab/catt

⁠Sample Test

We provide a test sample data testSample.fq for user to test their install.

docker run -t --rm -v $PWD:/output guobioinfolab/catt /catt/catt.py -f testSample.fq -o /output/testSampleoutput -t 2

A csv format file with name testSampleoutput.CATT.csv shoule be created in current folder.

⁠Usage

CATT can automatically detect input format, which could be sam/bam, fasta/fastq format.

### For sam/bam format, single-end input:
docker run -it --rm -v $PWD:/output -w /output guobioinfolab/catt /catt/catt.py [option] -f inputFile -o outputName
### For paired-end input:
docker run -it --rm -v $PWD:/output -w /output guobioinfolab/catt /catt/catt.py [option] -1 inputFile1 -2 inputFile2 -o outputName

Where $PWD is the path of folder contain your input data (absolute path, or just $PWD if input file is in current folder)

option:

• -t {numberOfThreads}: number of alignment threads. default: 16
• -sc : Using Single-Cell mode, which will filter out sequence error strictly. As some rare T cell would have special TCR (like doulbe-beta $\beta\beta$), CATT will not only keep one CDR3 sequence left, all sequences satisfied requirement will be kept.

⁠Output format

CATT will outputs a csv file (OutputName.CATT.csv) contain CDR3 sequences with their abundance, V, D and J genes segment and their bayes probability. The result file is like:

⁠FAQ

Q: Got permission denied while trying to connect to the Docker daem when try to build docker image

A: Make sure your user is in the docker group that have permission to use docker command

Copyright Guo Lab⁠ , College of Life Science and Technology⁠ , HUST⁠ , China