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.
- Create a new Conda environment:
conda create -n extractr_env python=3.9
- Activate the environment:
conda activate extractr_env
- Install Jellyfish:
conda install -c bioconda jellyfish
- 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 30
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
1 maintainer
Metadata
1 maintainer
Release files for extracTR 0.2.20
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| extracTR-0.2.20.tar.gz | 15.7 kB | Without provenance | Details |
Release files / extracTR-0.2.20.tar.gz
| Download URL | extracTR-0.2.20.tar.gz |
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| Size | 15.7 kB |
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