CATnip Workflow

CATnip a tool to assess nucleotide divergence and sequence resolution between user-defined categories.

Prerequisites

• Conda or Mamba
• Git

Installation (Recommended)

Install CATnip directly from Bioconda:

conda create -n catnip -c conda-forge -c bioconda catnip-seq
conda activate catnip

Or faster with mamba:

mamba create -n catnip -c conda-forge -c bioconda catnip-seq

Development Installation

1. Clone the repository:

   git clone https://github.com/CIBIO-BU/catnip
   cd catnip
   

2. Create the conda environment:

   conda env create -f catnip-env.yml
   

3. Activate the environment:

   conda activate catnip
   

4. Install catnip command:

   pip install -e .
   

5. Check help message:

   catnip -h
   

6. Run the test workflow:

   cd test-workflow
   catnip -i coi_micointf_mil.fasta -f coi_micointf_mil_mapping.tsv -c 0,1,2,3 -p 10
   

Environment Details

The conda environment includes:

• Python 3.11
• CD-HIT 4.8.1 (sequence clustering)
• Bowtie2 2.5.4 (sequence alignment)
• SAMtools (BAM/SAM file processing)
• pysam (Python interface for SAM/BAM files)
• pandas & numpy (data analysis)

Implementation Details

• Divergence values are rounded to the NEAREST WHOLE VALUE. However, output is presented with one decimal case.
• Taxa absent from the output file were excluded from the alignment step, as they can be reliably distinguished from all other taxa in the dataset based on the input divergence thresholds.