piscatorx/videre-pipeline

Pipeline for metranscriptome data

Videre

Videre is a nexflow computational pipeline for metatranscriptome data assembly and analysis.

Getting Started

The videre pipeline take raw RNA fastq reads and assembles them into a metatranscrptome. To get started clone/download this repository to your local machine and install the prerequisites in the list below.

Prerequisites

Nextflow

Nextflow requires Java to to run more details from https://www.nextflow.io/

Miniconda

Due to the multiple number of programs required for this pipeline miniconda is highly recommended for package and environment management.

Installing

All tools and dependencies used in this pipeline are listed in the videre.yml file. The environment may be created using conda env create -f videre.yml

Running the pipeline

The main pipeline scripts are

• videre.nf is the main nextflow pipeline script for sequence read assembly to generate the metascriptome.
• videre-salmon.nf is the nextflow script predicting the protein coding regions from the metatranscriptome.
• videre-diamond.nf is for annotating the protein coding regions and assigning taxonomy using the MMETSP database
• videre-hmmer.nf is for assigning Pfam (protein domain families) using hmmscan

Authors

• Andrew Ndhlovu