BBTools Guides
Comprehensive documentation and tutorials for BBTools suite
🎯 Core Tools Documentation
BBMap Guide
Complete guide to BBMap, the fast splice-aware read aligner. Learn about indexing, performance tuning, memory management, and advanced alignment options for DNA/RNA sequencing data.
BBDuk Guide
Master BBDuk for adapter trimming, quality filtering, and contamination removal. Covers kmer-based operations, memory usage, and parameter optimization for high-quality read preprocessing.
BBMerge Guide
Learn to merge paired-end reads using BBMerge's neural network approach. Understand overlap detection, false positive reduction, and optimal parameters for different sequencing platforms.
Tadpole Guide
Comprehensive tutorial for Tadpole assembler. Learn kmer-based assembly, error correction, read extension, and optimization for microbial genomes and organelles.
Clumpify Guide
Optimize file compression and processing speed with Clumpify. Learn how to group overlapping reads into clumps for better compression and faster downstream analysis.
BBNorm Guide
Master kmer-based coverage normalization with BBNorm. Learn to reduce coverage variation for better assemblies and remove sequencing errors based on kmer depth.
📊 Quality Control & Analysis
Stats Guide
Generate comprehensive statistics for sequence files. Learn to calculate N50, GC content, length distributions, and quality metrics for sequence analysis and QC.
FilterByTile Guide
Filter Illumina reads by flowcell tile quality. Learn to identify and remove reads from problematic tiles to improve overall data quality in Illumina sequencing runs.
CalcUniqueness Guide
Calculate genome uniqueness and complexity using kmer analysis. Understand repetitive regions, mappability, and genome complexity for better experimental design.
Preprocessing Guide
Complete preprocessing workflow for sequencing data. Learn best practices for quality trimming, adapter removal, contamination filtering, and data preparation pipelines.
🧹 Deduplication & Error Correction
Dedupe Guide
Remove duplicate sequences and PCR artifacts with Dedupe. Learn about optical duplicate detection, cluster-based deduplication, and memory-efficient processing.
Repair Guide
Fix broken paired-end read files with Repair. Learn to restore proper pairing, convert between paired formats, and handle orphaned reads in sequencing data.
🧬 Variant Calling & Analysis
CallVariants Guide
Comprehensive variant calling with CallVariants. Learn multisample analysis, ploidy handling, indel realignment, and VCF output for genomic variation detection.
🔬 Taxonomy & Classification
Taxonomy Guide
Work with NCBI taxonomy data in BBTools. Learn to download taxonomy files, convert accessions to TaxIDs, and use taxonomic information for sequence classification.
BBSketch Guide
Rapid taxonomic identification using MinHash sketches. Learn BBSketch and SendSketch for fast species identification and contamination detection in sequencing data.
Seal Guide
Alignment-free quantification with Seal. Learn kmer-based abundance estimation for RNA-seq, metagenomics, and rapid sequence quantification without mapping.
🔄 Format Conversion & Manipulation
Reformat Guide
Convert between sequence formats with Reformat. Learn format conversion, interleaving/deinterleaving, compression options, and sequence manipulation operations.
🛠️ Specialized Applications
BBMask Guide
Mask low-complexity and repetitive sequences with BBMask. Learn entropy-based masking, tandem repeat detection, and sequence complexity filtering techniques.
AddAdapters Guide
Add synthetic adapter sequences to reads for testing and validation. Learn adapter simulation, contamination testing, and preprocessing pipeline validation.
SplitNextera Guide
Process Nextera mate-pair libraries with SplitNextera. Learn to handle jumping libraries, transposase sequences, and mate-pair specific preprocessing steps.
📜 Reference & Legacy
Sample Guide Template
Template and example structure for BBTools guides. Useful for understanding guide format and as a reference for creating new documentation.
BBMap Legacy Documentation
Historical BBMap documentation and readme. Contains legacy information and early development notes for BBMap aligner reference.
About BBTools Guides
These comprehensive guides are written by Brian Bushnell, creator of BBTools, and provide detailed documentation for the complete suite of bioinformatics tools. Each guide includes:
- Detailed parameter explanations - Understand every option and flag
- Usage examples - Real-world command examples and workflows
- Best practices - Optimization tips and recommended approaches
- Memory and performance notes - Resource requirements and tuning advice
- Common troubleshooting - Solutions to frequently encountered issues
💡 Tips for Using These Guides
- Start with the BBDuk Guide for quality control basics
- Use the BBMap Guide for alignment fundamentals
- Consult the Preprocessing Guide for complete workflow examples
- Each tool's individual documentation page also links to its guide
- Guides are regularly updated - check the "Last updated" date in each file