openeuler/kb_python repository overview

⁠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:

⁠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.