satellome 1.6.1

A comprehensive tool for satellite DNA analysis in T2T genome assemblies

Satellome

A comprehensive bioinformatics tool for analyzing satellite DNA (tandem repeats) in telomere-to-telomere (T2T) genome assemblies.

Overview

Satellome integrates Tandem Repeat Finder (TRF) to identify, classify, and visualize repetitive DNA sequences, with a particular focus on centromeric and telomeric regions. It provides a complete pipeline from raw genome sequences to detailed visualizations and reports of tandem repeat patterns.

The tool is designed to work with various genome assembly projects including:

• T2T (Telomere-to-Telomere) Consortium assemblies
• DNA Zoo chromosome-length assemblies
• VGP (Vertebrate Genome Project) assemblies
• NCBI RefSeq and GenBank assemblies

Features

• Tandem Repeat Detection: Automated detection using TRF with optimized parameters
• Smart Classification: Categorizes repeats into microsatellites, complex repeats, and other types
• Rich Visualizations: Generates karyotype plots, 3D visualizations, and distance matrices
• Annotation Integration: Supports GFF3 and RepeatMasker annotations
• Parallel Processing: Efficient handling of multiple genomes
• Smart Pipeline: Automatically skips completed steps (override with --force)
• Compressed File Support: Direct processing of .gz compressed FASTA files
• K-mer Based Filtering: Optional k-mer profiling to focus on repeat-rich regions and skip repeat-poor areas

Installation

Prerequisites

• Python 3.9 or higher
• Conda (recommended) or pip
• TRF (Tandem Repeat Finder) binary

Quick Setup

1. Clone the repository

git clone https://github.com/aglabx/satellome.git
cd satellome

2. Create conda environment

conda create -n satellome python=3.9
conda activate satellome

3. Install dependencies

pip install -r requirements.txt

4. Install satellome

pip install -e .  # Development mode
# or
pip install .     # Production mode

Note: During installation, Satellome will automatically attempt to install external tools (FasTAN, tanbed, modified TRF). This process:

• Compiles tools from source (requires: git, make, gcc/clang)
• Installs binaries to <site-packages>/satellome/bin/ (or ~/.satellome/bin/ if no write permissions)
• Takes 2-5 minutes depending on your system
• Can be skipped: SATELLOME_SKIP_AUTO_INSTALL=1 pip install satellome
• If compilation fails, Satellome will still install successfully
• Failed tools can be installed later with satellome --install-all

5. Download TRF binary

# Linux
wget https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64
chmod +x trf409.linux64
mv trf409.linux64 trf

# macOS
wget https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.macosx
chmod +x trf409.macosx
mv trf409.macosx trf

TRF for Large Genomes (Chromosomes >1-2 GB)

Important: The standard TRF binary has limitations with very large chromosomes (>1-2 GB) and may crash during analysis. For large genome assemblies (e.g., some plant genomes, salamander genomes), use our modified TRF version.

Automatic Installation (Linux)

# Install modified TRF automatically (Linux only)
satellome --install-trf-large

Binary will be installed to <site-packages>/satellome/bin/trf-large (or ~/.satellome/bin/trf-large as fallback).

Note: Automatic installation works best on Linux. macOS users may encounter compilation issues and should use manual installation or pre-compiled binaries.

Manual Installation

# Clone and build modified TRF
git clone https://github.com/aglabx/trf.git
cd trf
mkdir build && cd build
../configure
make

# Copy to system or Satellome directory
cp src/trf ~/.satellome/bin/trf-large

For pre-compiled binaries, visit: https://github.com/aglabx/trf/releases

When to use the modified TRF:

• Working with genomes containing chromosomes larger than 1-2 GB
• Experiencing crashes or "Segmentation fault" errors with standard TRF
• Processing large plant or amphibian genomes

The modified TRF includes memory optimizations and can handle chromosomes up to several gigabases in size. Specify the path using: --trf ~/.satellome/bin/trf-large

FasTAN and tanbed (Optional)

Satellome supports FasTAN as an alternative tandem repeat finder. FasTAN and its companion tool tanbed can be automatically installed:

Automatic Installation

# Install FasTAN only
satellome --install-fastan

# Install tanbed only
satellome --install-tanbed

# Install both FasTAN and tanbed
satellome --install-all

Note: These tools are automatically installed during pip install satellome. Manual installation is only needed if automatic installation failed or was skipped.

Binaries will be installed to <site-packages>/satellome/bin/ (or ~/.satellome/bin/ as fallback).

Requirements for Installation

The automatic installer requires:

• git: For cloning repositories
• make: For building
• C compiler: gcc, clang, or cc

On macOS:

xcode-select --install

On Ubuntu/Debian:

sudo apt-get install build-essential git

On CentOS/RHEL:

sudo yum groupinstall 'Development Tools'
sudo yum install git

Manual Installation

If you prefer manual installation or encounter issues:

FasTAN:

git clone https://github.com/thegenemyers/FASTAN.git
cd FASTAN
make
cp FasTAN ~/.satellome/bin/fastan

tanbed:

git clone https://github.com/richarddurbin/alntools.git
cd alntools
make
cp tanbed ~/.satellome/bin/tanbed

Usage

Basic Command

# Note: Output directory must be an absolute path
satellome -i genome.fasta -o /absolute/path/to/output_dir -p project_name -t 8

Advanced Options

# With GFF3 annotations
satellome -i genome.fasta -o output_dir -p project_name -t 8 --gff annotations.gff3

# With RepeatMasker annotations
satellome -i genome.fasta -o output_dir -p project_name -t 8 --rm repeatmasker.out

# Force rerun all steps
satellome -i genome.fasta -o output_dir -p project_name -t 8 --force

# Smart recompute: only process chromosomes that failed TRF analysis
satellome -i genome.fasta -o output_dir -p project_name -t 8 --recompute-failed

# Custom TRF binary path (if not in PATH)
satellome -i genome.fasta -o /absolute/path/to/output_dir -p project_name -t 8 --trf /path/to/trf409.macosx

# Parallel processing of multiple genomes
python scripts/run_satellome_parallel.py -i genomes_list.txt -o results_dir -t 32

# With k-mer filtering to skip repeat-poor regions
satellome -i genome.fasta -o output_dir -p project_name -t 8 --use_kmer_filter

# Use pre-computed k-mer profile
varprofiler genome.fasta genome.varprofile.bed 17 100000 25000 20
satellome -i genome.fasta -o output_dir -p project_name -t 8 --kmer_bed genome.varprofile.bed

# Adjust k-mer threshold (default 90000)
satellome -i genome.fasta -o output_dir -p project_name -t 8 --use_kmer_filter --kmer_threshold 70000

# Continue with partial results if some TRF runs fail
satellome -i genome.fasta -o output_dir -p project_name -t 8 --continue-on-error

# Skip FasTAN analysis (run TRF only)
satellome -i genome.fasta -o output_dir -p project_name -t 8 --nofastan

# Skip TRF analysis (run FasTAN only)
satellome -i genome.fasta -o output_dir -p project_name -t 8 --notrf

Parameters

• -i, --input: Input FASTA file (supports .fa, .fasta, .fa.gz, .fasta.gz)
• -o, --output: Output directory (required, must be an absolute path)
• -p, --project: Project name (required)
• -t, --threads: Number of threads (default: 1)
• --gff: GFF3 annotation file (optional)
• --rm: RepeatMasker output file (optional)
• --trf: Path to TRF binary (default: "trf")
• --force: Force rerun all steps
• --recompute-failed: Smart recompute - only process chromosomes/contigs that failed TRF analysis (missing from results)
• --nofastan: Skip FasTAN analysis (TRF runs by default)
• --notrf: Skip TRF analysis (FasTAN runs by default)
• --use_kmer_filter: Enable k-mer based filtering of repeat-poor regions
• --kmer_threshold: Threshold for unique k-mers (default: 90000)
• --kmer_bed: Pre-computed k-mer profile BED file from varprofiler
• --continue-on-error: Continue pipeline even if some TRF runs fail (results may be incomplete)

Note: By default, both TRF and FasTAN run on every analysis. Use --nofastan or --notrf to skip either tool. At least one tool must run.

Output Structure

output_dir/
├── genome_name.trf                   # Main TRF output file
├── genome_name.gaps.bed              # Gaps annotation in BED format
├── genome_name.1kb.trf               # Repeats >1kb
├── genome_name.3kb.trf               # Repeats >3kb
├── genome_name.10kb.trf              # Repeats >10kb
├── genome_name.micro.trf             # Microsatellites (1-9 bp monomers)
├── genome_name.complex.trf           # Complex repeats (>9 bp monomers)
├── genome_name.pmicro.trf            # Potential microsatellites
├── genome_name.tssr.trf              # Tandem simple sequence repeats
├── genome_name.*.gff3                # GFF3 format files for each category
├── genome_name.*.fa                  # FASTA files with repeat sequences
├── distances.tsv.*                   # Distance matrices with various extensions
├── fastan/
│   ├── project_name.1aln             # FasTAN alignment output
│   └── project_name.bed              # FasTAN results in BED format
├── images/
│   ├── *.png                         # Karyotype and other visualizations
│   └── *.svg                         # Vector graphics versions
└── reports/
    ├── satellome_report.html         # Comprehensive HTML report
    └── annotation_report.txt         # Annotation intersection report (if GFF provided)

Note: The fastan/ directory and gap annotation file are generated by default. Use --nofastan to skip FasTAN analysis.

Classification System

Satellome classifies tandem repeats into four categories:

1. micro: Microsatellites (monomer length 1-9 bp)
2. complex: Complex repeats (monomer length >9 bp)
3. pmicro: Potential microsatellites
4. tssr: Tandem simple sequence repeats

Utility Scripts

Format Conversion

# Convert TRF to FASTA
python scripts/trf_to_fasta.py -i repeats.trf -o repeats.fasta

# Convert TRF to GFF3
python scripts/trf_to_gff3.py -i repeats.trf -o repeats.gff3

# Extract coordinates
python scripts/trf_to_coordinates.py -i repeats.trf -o coordinates.txt

Analysis Tools

# Check TRF consistency - verify all large scaffolds have results
python scripts/check_trf_consistency.py -f genome.fasta -t output_dir/genome.trf
python scripts/check_trf_consistency.py -f genome.fasta -t output_dir/genome.trf -s 500000 -o report.txt

# Extract large tandem repeats
python scripts/trf_get_large.py -i repeats.trf -m 1000 -o large_repeats.trf

# Get microsatellite statistics
python scripts/trf_get_micro_stat.py -i repeats.trf -o micro_stats.txt

# Check telomeric repeats
python scripts/check_telomeres.py -i genome.fasta -t repeats.trf

# Check TRF results consistency
python scripts/check_trf_consistency.py -f genome.fna -t genome.trf

# Batch check TRF consistency for multiple genomes
python scripts/batch_check_trf_consistency.py reptiles mammals birds

Quality Control Scripts

check_trf_consistency.py

Verifies that TRF analysis completed successfully for all contigs/scaffolds above a certain size threshold.

# Basic usage
python scripts/check_trf_consistency.py -f genome.fna -t genome.trf

# With custom minimum scaffold size (default: 1Mb)
python scripts/check_trf_consistency.py -f genome.fna -t genome.trf -s 500000

# With debug information for troubleshooting
python scripts/check_trf_consistency.py -f genome.fna -t genome.trf --debug

# Save detailed report
python scripts/check_trf_consistency.py -f genome.fna -t genome.trf -o report.txt

batch_check_trf_consistency.py

Batch process multiple genome assemblies to check TRF consistency.

# Check multiple directories
python scripts/batch_check_trf_consistency.py reptiles mammals birds

# Auto-skip failed assemblies
python scripts/batch_check_trf_consistency.py reptiles --auto-skip

# Show assemblies that need TRF analysis
python scripts/batch_check_trf_consistency.py reptiles --check-missing

# With progress tracking and debug info
python scripts/batch_check_trf_consistency.py reptiles --debug --verbose

# Save summary report
python scripts/batch_check_trf_consistency.py reptiles -o consistency_report.txt

Interactive mode options:

• [s] Skip - continue to next assembly
• [d] Delete - remove TRF directory and re-run TRF
• [v] View - show TRF directory contents
• [q] Quit - exit the script

Smart Recompute Mode

If TRF analysis fails for some chromosomes (e.g., due to memory issues or signal errors), you can use the --recompute-failed flag to reprocess only the failed chromosomes without redoing the entire analysis.

How it works:

1. Checks which chromosomes/contigs are missing from existing TRF results
2. Extracts only those chromosomes to a temporary FASTA file
3. Runs TRF only on the missing chromosomes
4. Merges results back into the existing TRF file
5. Continues with the rest of the pipeline

Usage example:

# First, check which chromosomes failed
python scripts/check_trf_consistency.py -f genome.fna -t output_dir/project.trf

# Then recompute only the failed ones
satellome -i genome.fasta -o output_dir -p project_name -t 8 --recompute-failed

When to use:

• TRF failed for specific chromosomes (visible in error messages like "TRF failed for 94.fa")
• check_trf_consistency.py reports missing chromosomes
• You want to save time by not reprocessing successful chromosomes

Benefits:

• Much faster than --force (only processes failed chromosomes)
• Preserves successful results
• Creates automatic backup before merging (.before_recompute suffix)
• More informative error messages with actual TRF output

Example Workflow

1. Download Test Dataset

# Download S. cerevisiae genome
curl -OJX GET "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/GCF_000146045.2/download?include_annotation_type=GENOME_FASTA,GENOME_GFF&filename=GCF_000146045.2.zip" -H "Accept: application/zip"
unzip GCF_000146045.2.zip

2. Run Analysis

# Run satellome pipeline
satellome -i ncbi_dataset/data/GCF_000146045.2/GCF_000146045.2_R64_genomic.fna \
          -o results \
          -p scerevisiae \
          -t 8 \
          --gff ncbi_dataset/data/GCF_000146045.2/genomic.gff

# View results
open results/scerevisiae_report.html

3. Analyzing DNA Zoo Assemblies

# Download a DNA Zoo assembly (example: Cheetah)
wget https://dnazoo.s3.wasabisys.com/Acinonyx_jubatus/aciJub1_HiC.fasta.gz

# Run satellome directly on compressed file (no need to decompress!)
satellome -i aciJub1_HiC.fasta.gz \
          -o dnazoo_results \
          -p cheetah \
          -t 8

Configuration

The pipeline uses settings.yaml for tool parameters. Key settings include:

• TRF parameters (match/mismatch scores, indel penalties)
• Minimum/maximum repeat lengths
• Classification thresholds
• Visualization parameters

Testing

Run the test suite:

python tests/test_overlapping.py
python test_standalone.py
python test_chromosome_sorting.py

Contributing

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Commit your changes (git commit -m 'Add amazing feature')
4. Push to the branch (git push origin feature/amazing-feature)
5. Open a Pull Request

Citation

If you use Satellome in your research, please cite:

Komissarov A. et al. (2024). Satellome: A comprehensive tool for satellite DNA 
analysis in T2T genome assemblies. [Publication details]

License

This project is licensed under the MIT License - see the LICENSE file for details.

Support

• Issues: GitHub Issues
• Documentation: Wiki
• Email: [e-mail]

Acknowledgments

• Tandem Repeat Finder by Gary Benson
• T2T Consortium for inspiring this work
• DNA Zoo for providing chromosome-length assemblies
• Vertebrate Genome Project for high-quality reference genomes