extracTR

Introduction

extracTR is a tool for identifying and analyzing tandem repeats in genomic sequences. It works with raw sequencing data (FASTQ) or assembled genomes (FASTA), using k-mer based approaches to detect repetitive patterns efficiently.

Features

• Efficient tandem repeat detection from raw sequencing data
• Support for single-end and paired-end FASTQ files
• Support for genome assemblies in FASTA format
• Customizable parameters for fine-tuning repeat detection
• Output in easy-to-analyze CSV format
• Multi-threaded processing for improved performance

Requirements

• Python 3.7 or later
• Jellyfish 2.3.0 or later
• Conda (for easy environment management)

Installation

We recommend installing extracTR in a separate Conda environment to manage dependencies effectively.

1. Create a new Conda environment:

conda create -n extractr_env python=3.9

2. Activate the environment:

conda activate extractr_env

3. Install Jellyfish:

conda install -c bioconda jellyfish

4. Install extracTR using pip:

pip install extracTR

To deactivate the environment when you're done:

conda deactivate

Usage

Before running extracTR, ensure that you have removed adapters from your sequencing reads and activated the Conda environment:

conda activate extractr_env

Basic usage:

For paired-end FASTQ files:

extracTR -1 reads_1.fastq -2 reads_2.fastq -o output_prefix -c 30

For single-end FASTQ file:

extracTR -1 reads.fastq -o output_prefix -c 30

For genome assembly in FASTA format:

extracTR -f genome.fasta -o output_prefix -c 1

Advanced usage with custom parameters:

extracTR -1 reads_1.fastq -2 reads_2.fastq -o output_prefix -t 64 -c 30 -k 25

Options:

• -1, --fastq1: Input file with forward DNA sequences in FASTQ format
• -2, --fastq2: Input file with reverse DNA sequences in FASTQ format (optional for paired-end data)
• -f, --fasta: Input genome assembly in FASTA format
• -o, --output: Prefix for output files
• -t, --threads: Number of threads to use (default: 32)
• -c, --coverage: Coverage to use for indexing (required)
• -k, --k: K-mer size to use for indexing (default: 23)
• --lu: Coverage cutoff for k-mers (default: 100 * coverage)

Note: You must provide either FASTQ file(s) or a FASTA file as input.

Output

extracTR generates the following output files:

• {output_prefix}.csv: Main output file containing detected tandem repeats
• {output_prefix}.sdat: Intermediate file with k-mer frequency data
• Additional files for detailed analysis and debugging