Comprehensive Guides and References
Everything you need to master the BBTools suite
Complete overview of BBTools with installation instructions, script descriptions, and author information. Start here for a comprehensive introduction.
Essential guide covering system requirements, installation, standard syntax, file formats, memory settings, and common parameters across all tools.
Concise descriptions of all BBTools organized by category: alignment, assembly, QC, filtering, and specialized analysis tools.
Complete guide for the splice-aware short read aligner. Covers alignment parameters, index building, variant calling workflows, and performance optimization.
Comprehensive guide for adapter trimming, quality filtering, and contaminant removal. Includes parameter explanations, common workflows, and troubleshooting tips.
Guide for merging overlapping paired-end reads using neural networks. Covers merger parameters, quality settings, and integration with other tools.
Complete documentation for the fast assembler and error corrector. Includes assembly strategies, kmer selection, and optimization for different data types.
Guide for kmer-based coverage normalization. Covers normalization strategies, target coverage selection, and preprocessing for assembly.
Documentation for read reordering and deduplication. Includes compression strategies, duplicate removal, and memory-efficient processing of large datasets.
Step-by-step guide for read preprocessing workflows. Covers quality assessment, adapter removal, filtering, and preparation for downstream analysis.
Guide for sequence statistics and quality assessment. Includes assembly metrics, coverage analysis, and data quality evaluation methods.
Complete guide for file format conversions, subsampling, and sequence manipulation. Covers FASTA/FASTQ processing and data preparation.
Documentation for fixing broken paired-end read files. Covers pair restoration, orphan handling, and file integrity checking.
Guide for removing low-quality reads based on flowcell position. Includes tile-based filtering strategies and quality improvement methods.
Comprehensive guide for variant calling from aligned reads. Covers SNP detection, indel calling, quality filtering, and VCF output formatting.
Guide for fast taxonomic identification using MinHash sketching. Includes database selection, classification workflows, and result interpretation.
Complete guide for taxonomic analysis and classification. Covers NCBI taxonomy integration, classification workflows, and result filtering.
Documentation for sequence matching and quantification. Includes RNA-seq quantification, contamination detection, and kmer-based analysis.
Guide for duplicate and contained sequence removal. Covers clustering strategies, similarity thresholds, and memory-efficient processing.
Documentation for calculating sequence uniqueness and complexity. Includes repeat analysis, mappability assessment, and genome complexity metrics.
Guide for sequence masking based on complexity, repeats, or custom criteria. Includes low-complexity filtering and reference preparation.
Specialized guide for processing Nextera long mate pair libraries. Covers junction detection, splitting strategies, and quality assessment.
Documentation for adding adapter sequences to reads. Includes synthetic read preparation and adapter sequence design.
Template and example for creating custom analysis workflows. Includes best practices for tool integration and parameter optimization.
Primary documentation file with installation instructions, basic usage examples, and links to additional resources.
Documentation for configuration files, environment variables, and advanced setup options for enterprise deployments.
Comprehensive guide to supported file formats, compression options, and format-specific parameters across all BBTools.
Instructions for compiling BBTools from source code, including dependency requirements and platform-specific considerations.
Version control information, development workflow, and instructions for contributing to BBTools development.
Technical guide for server deployment, including taxonomy servers, sketch servers, and distributed computing configurations.
Historical documentation for BBMap, including original usage examples and legacy parameter explanations for backward compatibility.
Detailed documentation for Count-Min Sketch-based error correction, including algorithm details and performance characteristics.
Complete version history with detailed changes, bug fixes, new features, and performance improvements across all BBTools releases.
Proper citation formats for BBTools in academic publications, including specific citations for individual tools and the overall suite.
Complete licensing information, copyright notice, and terms of use for BBTools suite. Includes government licensing and distribution rights.
Special legal notice regarding Illumina-specific components and any third-party licensing considerations for sequencing platform integration.
Browse all documentation files directly on GitHub, including any updates or additional files not listed above.
Production-ready pipeline scripts and workflow examples demonstrating best practices for combining multiple BBTools.
Report issues, ask questions, and connect with the BBTools community on GitHub. Search existing issues for solutions.
Access the official BBTools taxonomy server for species identification and classification services used by SendSketch and related tools.