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https://github.com/bimberlab/nimble

nimble — execute lightweight, flexible alignments on custom reference libraries

https://github.com/bimberlab/nimble

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    Academic publication links
    Links to: ncbi.nlm.nih.gov
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    Academic email domains
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary

Keywords

alignment bioinformatics cli immunology python3 rna-seq-pipeline rust-lang scrna-seq
Last synced: 5 months ago · JSON representation

Repository

nimble — execute lightweight, flexible alignments on custom reference libraries

Basic Info
  • Host: GitHub
  • Owner: BimberLab
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 215 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 0
  • Open Issues: 6
  • Releases: 0
Topics
alignment bioinformatics cli immunology python3 rna-seq-pipeline rust-lang scrna-seq
Created over 5 years ago · Last pushed 8 months ago
Metadata Files
Readme License

README.md

nimble

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.

nimble_scrnaseq_pipeline

Documentation

For installation instructions, see below. Detailed documentation, including usage instructions and a custom HLA reference vignette, can be found at the wiki.

Support

Please open an issue on this repository for feature requests, support for additional operating systems, bugfixes, or questions.

Installation

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 musl package, 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.

Other resources

  • The nimbler package contains R routines for integrating nimble data into a Seurat object.

  • The source code for the backend aligner can be found here.

References and Credits

rust-pseudoaligner

Samtools and HTSlib

Köster, J. (2016). Rust-Bio: a fast and safe bioinformatics library. Bioinformatics, 32(3), 444-446.

Cock, P.J. et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), pp.1422–1423.

Owner

  • Name: Bimber Lab
  • Login: BimberLab
  • Kind: organization

Software created by the Bimber Lab of OHSU

GitHub Events

Total
  • Issues event: 6
  • Watch event: 1
  • Delete event: 10
  • Issue comment event: 4
  • Push event: 35
  • Gollum event: 22
  • Pull request event: 14
  • Create event: 4
Last Year
  • Issues event: 6
  • Watch event: 1
  • Delete event: 10
  • Issue comment event: 4
  • Push event: 35
  • Gollum event: 22
  • Pull request event: 14
  • Create event: 4

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 6
  • Total pull requests: 4
  • Average time to close issues: over 2 years
  • Average time to close pull requests: 14 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 1
  • Bot pull requests: 2
Past Year
  • Issues: 4
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 14 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 1
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • bbimber (4)
  • hextraza (1)
Pull Request Authors
  • dependabot[bot] (6)
  • bbimber (4)
Top Labels
Issue Labels
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dependencies (6) python (1)

Dependencies

requirements.txt pypi
  • biopython ==1.78
  • certifi ==2020.12.5
  • chardet ==4.0.0
  • distro ==1.5.0
  • idna ==2.10
  • numpy ==1.22.0
  • pandas ==1.2.0
  • pysam ==0.16.0.1
  • python-dateutil ==2.8.1
  • pytz ==2020.5
  • requests ==2.25.1
  • six ==1.15.0
  • urllib3 ==1.26.5
setup.py pypi
  • requests *
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/docker.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v3.2.0 composite
  • docker/login-action v2.1.0 composite
  • docker/metadata-action v4 composite
  • docker/setup-buildx-action v2.2.1 composite
  • docker/setup-qemu-action v2.1.0 composite
Dockerfile docker
  • centos 7 build