nimble is a lightweight tool designed to supplement standard RNA-seq and scRNA-seq pipelines by providing accurate gene quantification with customizable reference libraries. Traditional transcript quantification methods align reads to a single reference genome and apply a uniform feature-calling approach across all genes. While effective in most cases, this method can introduce systematic inaccuracies, particularly for complex or highly variable gene families such as MHC and KIR, where standard approaches may result in misalignment, lost counts, or incorrect feature assignments. Nimble addresses these gaps by allowing you to define custom gene spaces with configurable scoring criteria, ensuring more accurate and biologically relevant quantification.
For installation instructions, see below. Detailed documentation, including usage instructions and a custom HLA reference vignette, can be found at the wiki.
Please open an issue on this repository for feature requests, support for additional operating systems, bugfixes, or questions.
The best way to install nimble is via our Docker image.
To install the latest nimble Docker image, run:
docker pull ghcr.io/bimberlab/nimble:latest
Alternatively, you can install nimble through pip. Nimble requires Python 3 and samtools. Currently, we support the following operating systems:
- MacOS
- Linux distributions with musl support, i.e. Alpine and Debian/Ubuntu with the
muslpackage, etc.
To install nimble with pip, run:
pip install git+https://github.com/BimberLab/nimble
Once you have nimble installed, proceed to our usage documentation.
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The nimbler package contains R routines for integrating nimble data into a Seurat object.
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The source code for the backend aligner can be found here.
Köster, J. (2016). Rust-Bio: a fast and safe bioinformatics library. Bioinformatics, 32(3), 444-446.