guobioinfolab/catt
guobioinfolab
An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences
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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:
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HomePage: [***]
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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.
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Download and install Docker, https://www.docker.com/
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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.
Shell### 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:
| CDR3seq | Sequence | V-region | J-region | Frequency | Probability |
|---|---|---|---|---|---|
| CASTPWGGNEQFF | TGT......TTC | TRBV9*03 | TRBJ2-1*01 | 67236 | 0.0012 |
| ... | ... | ... | ... | ... | ... |
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
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