BBRename

About This Tool

The rename tool (accessible via both rename.sh and bbrename.sh) renames sequencing reads using the jgi.RenameReads class with multiple concurrent processing strategies:

• Sequential numbering: Uses ConcurrentReadInputStream and ConcurrentReadOutputStream to rename reads to <prefix>_<number> format with thread-safe counter incrementing
• Insert size renaming: Calculates insert sizes via Read.insertSizeMapped() method and integrates with FASTQ.PARSE_CUSTOM for custom header generation
• Coordinate-based renaming: Uses IlluminaHeaderParser2.parse() and appendCoordinates() methods to extract and reformat Illumina coordinate information
• Header trimming: Implements trim() and trimBeforeSymbol() methods with configurable left/right character removal and symbol-based trimming using lastIndexOf() operations
• SRA header fixing: Uses spacePattern.split() with regex "\\s+" to parse SRA headers and extract Illumina identifiers from formatted strings

Memory Management: Utilizes ListNum<Read> collections with concurrent processing, ByteBuilder for efficient string construction, and optional Quantizer.quantize() for quality score compression.

For complete parameter documentation and examples, see the full RENAME documentation.

Basic Usage

# Both commands work identically via jgi.RenameReads:
bbrename.sh in=reads.fq out=renamed.fq prefix=sample
rename.sh in=reads.fq out=renamed.fq prefix=sample

# Advanced renaming modes supported:
bbrename.sh in=reads.fq out=renamed.fq renamebyinsert=t
bbrename.sh in=reads.fq out=renamed.fq renamebycoords=t fixsra=t
bbrename.sh in=reads.fq out=renamed.fq trimleft=10 trimright=5

Processing Architecture: Both scripts invoke java -cp bbmap.jar jgi.RenameReads with 4-buffer concurrent I/O streams, automatic format detection via FileFormat.testInput(), and configurable compression levels through ReadWrite.setZipThreads().

Support

For questions and support:

• Email: bbushnell@lbl.gov
• Documentation: bbmap.org