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Overview of nimble

nimble is a fast, accurate, and configurable RNA sequence aligner that executes lightweight alignments on arbitrary reference libraries. It uses pseudo-alignment to rapidly generate supplemental calls to complement a data pipeline's primary alignment. It does this with low overhead, making it possible to run supplemental alignments on any machine.

The nimble workflow involves three steps:

1. Generate a nimble library from .fasta or .csv data, which can contain arbitrary metadata for use further down the pipeline
2. Align a nimble library to single or double-paired .fastq data, or a 10x .bam file
3. Filter the alignment output with a suite of post-processing algorithms

Getting Started

• Installation
• Quickstart and Usage
• System Requirements
• Example Data Analysis
• Libraries
• Issues

Config and Options

• Environment Variables
• Reporting Methods

Specifications

• Input Formats
• Library File Format
• Debug Output Format

Other Links

• Docker Container
• Backend Aligner