Quickstart

Installation

nimble only requires Python3 and samtools.

To install from source, run pip install git+https://github.com/BimberLab/nimble.

Alternatively, you can use the docker package via docker pull ghcr.io/bimberlab/nimble:latest.

Usage

To perform an alignment of RNA data against your reference library, do the following:

1. Run python -m nimble generate [<reference-library.fasta> | <reference-library.csv> | <reference-library.fasta> <reference-library.csv>] <output.json>. This command takes either a .fasta file, a .csv file with "name" and "sequence" columns, or a .fasta and a .csv without the "sequence" column. Any additional fields in the .csv will be maintained in the library as metadata. The resulting library will be stored in output.json.

2. Run python -m nimble align <output.json> <results.tsv> [<input-r1.fastq> | <input.bam> | <input-r1.fastq> <input-r2.fastq>]. <output.json> is the file created by the generate command in the previous step.<input-r1.fastq> and <input-r2.fastq> are paths to your input bulk-seq data (<input-r2.fastq> is optional). Alternatively, you can provide a single .bam file. <results.tsv> is the path to your output results.

3. Run python -m nimble filter <method> <method parameters> <input.tsv> <output.tsv> to further process the results with one of the reporting methods.

The download command downloads the most recent aligner release. You can optionally specify a release version like so: python -m nimble download <version> where <version> is a release tag like "v0.0.1" or "v0.0.1-beta.1". The aligner is stored in the nimble python package directory. You shouldn't need to do this, unless you're trying to get a specific version of the aligner -- align automatically downloads the latest version, which is usually what you want.

To get help information, run python -m nimble or python -m nimble help.