Quick reference
- The official kb_python docker image.
- Maintained by: openEuler CloudNative SIG.
- Where to get help: openEuler CloudNative SIG, openEuler.
kb_python | openEuler
kb_python is a Python wrapper for the kallisto | bustools single-cell RNA-seq pre-processing workflow, developed and maintained by Pachterlab. kb_python provides:
- Transcriptome index building (kb ref) from genome FASTA and GTF annotation files.
- Pseudoalignment and count matrix generation (kb count) for single-cell FASTQ files.
- Gene/transcript read extraction (kb extract) from pseudoalignment results.
- Built-in presets for multiple sequencing technologies (10xv2, 10xv3, Drop-seq, SMART-seq, etc.).
- kallisto and bustools binaries bundled with the package — no separate installation required.
- Source compilation of kallisto and bustools via kb compile for custom builds.
- Prebuilt reference indices available for common model organisms.
- Unified workflow for single-cell RNA-seq quantification and RNA velocity estimation. Learn more at kb_python.
Supported tags and respective Dockerfile links
The tag of each kb_python docker image is consist of the version of kb_python and the version of basic image. The details are as follows:
| Tags | Currently | Architectures |
|---|---|---|
| 0.30.2-oe2403sp3 | kb_python 0.30.2 on openEuler 24.03-LTS-SP3 | amd64, arm64 |
Usage
- Ensure that you have Docker installed, or are using Docker for Linux containers if on Windows.
- Obtain the kb_python docker image from DockerHub:
docker pull openeuler/kb_python:{Tag} - Run the Docker container to launch the kb_python environment.
docker run -it openeuler/kb_python:{Tag} - Verify the installation inside the container:
kb info
Question and answering
If you have any questions or want to use some special features, please submit an issue or a pull request on openeuler-docker-images.