widdowquinn / ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes

ideel

Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes.

• Original author: Mick Watson
• Original blog post: "Stop Publishing Bad Genomes", Mick Watson (2018)
• Original repository: mw55309/ideel

ideel is a snakemake workflow that processes a set of genomes (the input) and predicts coding sequences (CDS) with the prodigal gene-calling software.

The conceptual translations for these sequences are compared to (by default) the complete SWISSPROT database using the diamond sequence search tool. If you do not have a copy of this, it will be downloaded and prepared for you.

The length of each query protein is compared to its best SWISSPROT hit, and a query length/hit length ratio calculated.

Two histograms are produced, showing the distribution of this ratio for all predicted conceptual translations.

The tool is useful to help diagnose genome assemblies where there are a significant proportion of truncated coding sequences, having a premature stop codon. This can be a feature of long-read-only assemblies. Candidates are shown in the histogram as the proteins with query length/hit length ratio <≈ 0.9.

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Dependencies

• Snakemake
• Prodigal
• Diamond
• R

How to use this tool

0. (Optionally) create a conda environment

Creating a conda environment is a quick and effective way to manage software and dependency installation. To create a new environment with all the dependencies for ideel, you could use the commands:

conda create --name ideel python=3.8 -y
conda activate ideel
conda install snakemake prodigal diamond r -y

1. Clone this repository

You can use git to clone the repository:

git clone [e-mail]:widdowquinn/ideel.git

Alternatively, you can download the repository as a .zip file and extract it to your local hard drive:

wget https://github.com/widdowquinn/ideel/archive/refs/heads/master.zip
unzip master.zip

2. Change directory to the repository root

Then, at the command-line/terminal, issue:

cd ideel

3. Run ideel

By default ideel expects your input genomes to be in the directory genomes under the repository root. Create that directory, and place your genomes in it. Then issue the following command to run snakemake at the command-line:

snakemake -jN

where N is the number of threads you would like ideel to use.

The output files (histograms of the counts of genomes that match the sequence database with the indicated query length/hit length ratio) are placed by default in the directory figures.