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Assessing Evolutionary rates for multiple genomes

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CorEvol

CorEvol is a lightweight Python pipeline to calculate ω (dN/dS) values for the core genome of multiple genomic CDS sequences. The general workflow is described in the flowchart below.

Table of Contents

General Info

CorEvol processes a folder of your genomic CDS files and outputs the ω (dN/dS) values of the core, non-redundant, non-recombinant sequences, along with other useful files and folders. See Usage for more details.

graph LR
    subgraph Input Files
        A[seq1.fna, seq2.fna, ..., seqN.fna]
    end
    A --> B((Clustering<br/>&<br/>Redundancy removal))
    B --> C[Core Clusters]
    C --> X((Alignment))
    X --> Y[Aligned Core Clusters]
    Y --> D((Recombination<br/>Detection))
    D --> E[Recombinant Seqs.]
    D --> F[Non Recombinant Seqs.]
    F --> G[ω of core,<br/>non-redundant,<br/>non-recombinant<br/>clusters]
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Installation

The latest version of CorEvol is available here

Dummy installation

  1. Create a conda environment.
conda create -n corevol_env python=3.8
conda activate corevol_env
  1. Install OpenRDP in the said environment.
conda install -c bioconda openrdp
  1. Clone the CorEvol repository.
git clone https://github.com/AbhishakeL/CorEvol.git
cd corevol
  1. Install required Python packages.
pip install -r requirements.txt

Usage

To use CorEvol, run the following command to get to know of all the available parameters and options:

python CorEvol.py -h

Usage options:

python CorEvol.py -h
usage: CorEvol.py [-h] -i DIRECTORY -o OUTPUT [-p PATH] [-c IDENTITY]
                  [-d LENGTH_DIFF] [-sc LENGTH_CUTOFF] [-aL ALIGN_COV_LONG]
                  [-aS ALIGN_COV_SHORT] [-g MEMORY] [-n WORD_LENGTH]
                  [-pC PHYLOGENY_CUTOFF] [-r RDP_CONFIG] [-x COUNTS]
                  [-t THREADS]

Pipeline for running CorEvol.

options:
  -h, --help            show this help message and exit
  -i DIRECTORY, --directory DIRECTORY
                        Directory containing the FASTA files
  -o OUTPUT, --output OUTPUT
                        Directory containing the output files
  -p PATH, --path PATH  Path where the cdhit program is located
  -c IDENTITY, --identity IDENTITY
                        Sequence identity threshold (default: 0.9)
  -d LENGTH_DIFF, --length_diff LENGTH_DIFF
                        Length difference cutoff (default: 0)
  -sc LENGTH_CUTOFF, --length_cutoff LENGTH_CUTOFF
                        Length difference cutoff in amino acid (default: 1)
  -aL ALIGN_COV_LONG, --align_cov_long ALIGN_COV_LONG
                        Alignment coverage for longer sequence (default: 0.9)
  -aS ALIGN_COV_SHORT, --align_cov_short ALIGN_COV_SHORT
                        Alignment coverage for shorter sequence (default: 0.9)
  -g MEMORY, --memory MEMORY
                        Maximum available memory in GB (default: 1)
  -n WORD_LENGTH, --word_length WORD_LENGTH
                        Word length (default: 9)
  -pC PHYLOGENY_CUTOFF, --phylogeny_cutoff PHYLOGENY_CUTOFF
                        Minimum length of nucleotides prior to alignment
                        (default : 300)
  -r RDP_CONFIG, --rdp_config RDP_CONFIG
                        Path where internal parameters of RDP scanner is saved
  -x COUNTS, --counts COUNTS
                        Number of different RDP testing methodology used to
                        confidently conclude a sequence to be recombinant
                        (default: 4, max: 6)
  -t THREADS, --threads THREADS
                        Number of threads (default: 4)

Typical Usage

We strongy recommend running CorEvol.py from SPYDER Ipython terminal. This recommendation is mostly to circumnavigate a bug in the codeml package.

%run CorEvol.py -i ./Test -o ~/Out

The output folder contains the following files and folders.

Name Type Content
Neutral_Selection Directory A directory containing all the cluster of sequences that have undergone neutral selection event
NonRecombination_files Directory A directory containing _results.csv : Recombination detection output file, _formatted.phy and _tree.nwk files needed to run codeml for each of the clusters where recombination is not detected
Positive_Selection Directory A directory containing all the cluster of sequences that have undergone positive selection event
Purifying_Selection Directory A directory containing all the cluster of sequences that have undergone negative selection event
Recombination_Clusters Directory A directory containing _results.csv : Recombination detection output file for each of the clusters where recombination is detected
concatenated_seq.aln File ClustalW format alignment file for all the core, non-redundant, non-recombinant sequences, joined end to end
concatenated_seq.fas File FASTA format alignment file for all the core, non-redundant, non-recombinant sequences, joined end to end
Pan_matrix.xlsx File CD-HIT output, gnerated in amtrix format such that each row represent Cluster number and each column represent each sample. Background color of each row selected such that green represent ω >= 1,blue represent ω = 0, red represent ω < 1. Those without color are non-core/recombinant clusters
RDP_error.tsv File Cluster numbers for which Recombination could not be detected because there were less than three unique sequences in the cluster
Selection_table.tsv File A matrix with ω value for the clusters

License

This project is licensed under the GNU GPLv3 License. See the LICENSE file for details.

This README file includes more detailed instructions for installation and usage, and it ensures that the content is well-organized and easy to follow.

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