README.md

SRUFinder

Detect and subtype Single Repeat Units, mini-arrays, and CRISPR arrays by repeat matching with a comprehensive repeat sequence database

Table of contents

1. Quick start
2. Installation
3. SRUFinder

Quick start

conda create -n srufinder -c conda-forge -c bioconda -c russel88 srufinder
conda activate srufinder
srufinder my.fasta my_output

Installation

SRUFinder can be installed either through conda or pip.

It is advised to use conda, since this installs SRUFinder and all dependencies, and downloads with database in one go.

Conda

Use miniconda or anaconda to install.

Create the environment with SRUFinder and all dependencies and database

conda create -n srufinder -c conda-forge -c bioconda -c russel88 srufinder

pip

If you have the dependencies (Python >= 3.8, Prodigal >= 2.6) in your PATH you can install with pip

Install srufinder python module

python -m pip install srufinder

Upgrade srufinder python module to the latest version

python -m pip install srufinder --upgrade

When installing with pip, you need to download the database manually:

# Download
svn checkout https://github.com/Russel88/SRUFinder/trunk/data

# Tell SRUFinder where the data is:
# either by setting an environment variable (has to done for each terminal session, or added to .bashrc):
export SRUFINDER_DB="/path/to/data/"
# or by using the --db argument each time you run SRUFinder:
srufinder input.fa output --db /path/to/data/

SRUFinder - How to

SRUFinder takes as input a nucleotide fasta, and produces outputs with SRU predictions

Activate environment

conda activate srufinder

Run with a nucleotide fasta as input

srufinder genome.fa my_output

For metagenome assemblies and short contigs/plasmids/phages, change the prodigal mode

The default prodigal mode expects the input to be a single draft or complete genome

srufinder assembly.fa my_output --prodigal meta

Check the different options

srufinder -h