catnip-seq 0.1.6

Explore nucleotide divergence and sequence resolution across user-defined categories.

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)

Documentation

Divergence values are rounded to the NEAREST WHOLE VALUE. However, output is presented with one decimal case.