LyRic

LyRic is a versatile automated transcriptome annotation and analysis workflow written in the Snakemake language. Its core functionality is the production of:

1. a set of high-quality RNA Transcript Models (TMs) mapped onto a genome sequence, based on Long-Read (LR) RNA sequencing data.
2. various summary statistics plots and analysis results that describe the input and output data in details
3. an interactive HTML table reporting statistics for each input sample, enabling easy and intuitive sample-to-sample comparison
4. a UCSC Track Hub to display output TMs, as well as various other tracks produced by LyRic.

(Note that features 2, 3 and 4 can be easily switched on and off).

LyRic is platform-agnostic, i.e. it can deal with FASTQ data coming from both the ONT and PacBio platforms.

Full LyRic documentation is here.

Quickstart

Prerequisites

• Anaconda installation (miniconda/mambaforge)
• Snakemake v8
• Singularity

[!NOTE]
It looks like Snakemake needs an installation of Anaconda even when the pipeline runs in a containerized environment

[!TIP] If you use Pixi to install your conda environments you can use the provided pixi.toml file to setup Snakemake and other requirements. Just run the following command from the pipeline directory:

pixi install

Get the pipeline

Clone the GitHub repo to the folder you want to use as the working directory of the pipeline and move to it:

git clone https://github.com/guigolab/LyRic lyric_test

cd lyric_test

Make a test run

The pipeline repository contains a small datasets that can be used for testing. You can run the pipeline on the test dataset with the following command:

snakemake --cores all

Execution shall take < half an hour.