How bbushnell/bbtools works
BBTools is a suite of independent command-line bioinformatics tools, not one end-to-end application. Its principal user workflow is to provide sequencing reads (and, where needed, references or databases), run a tool suited to the task, and receive processed reads, alignments, assembly output, or analysis results. Major documented branches include read mapping, quality control, correction, assembly, and read organization; the tree also shows barcode demultiplexing, coverage analysis, and clade/sketch search. The README documents capabilities beyond the sampled source, so this map shows tool-level workflows rather than unverified internal call chains.
Main entry points: SendClade.java Remote organism search · DemuxClient.java Barcode demultiplexing · BBMap.java BBMap mapping · CoveragePileup.java Coverage analysis
Components 22
Mapping and analysis
- BBMap mapping
current/align2/BBMap.java - Coverage analysis
current/jgi/CoveragePileup.java
Read preparation
- Trim and filter
current/bbduk/BBDuk3.java - Normalize and correct
current/bloom/BloomFilterCorrectorWrapper.java - Paired-read merging
- Read organization
current/clump/Clumpify.java
Assembly
- Tadpole assembly
current/assemble/Tadpole.java
Sketch and taxonomy
- Remote organism search
current/clade/SendClade.java - Ranked matches
current/clade/QueryResult.java
Other workflows
- Barcode demultiplexing
current/barcode/DemuxClient.java
Other components
- Sequencing user
- Reads and references
- Mapped reads
- Coverage reports
- Cleaned reads
- Corrected reads
- Merged reads
- Organized reads
- Assembly output
- Clade search service
- Demultiplexing service
- Barcode assignments
Connections 21
- Sequencing user → Reads and references: provides
- Reads and references → BBMap mapping: map against reference
- BBMap mapping → Mapped reads: writes alignments
- Mapped reads → Coverage analysis: analyze coverage
- Coverage analysis → Coverage reports: reports coverage
- Reads and references → Trim and filter: trim and filter
- Trim and filter → Cleaned reads: writes reads
- Reads and references → Normalize and correct: correct or normalize
- Normalize and correct → Corrected reads: writes reads
- Reads and references → Paired-read merging: merge pairs
- Paired-read merging → Merged reads: writes merged reads
- Reads and references → Read organization: reorder reads
- Read organization → Organized reads: writes reads
- Reads and references → Tadpole assembly: assemble or correct
- Tadpole assembly → Assembly output: writes results
- Sequencing user → Remote organism search: submit organism query
- Remote organism search → Clade search service: queries remotely
- Remote organism search → Ranked matches: returns matches
- Reads and references → Barcode demultiplexing: submit barcode data
- Barcode demultiplexing → Demultiplexing service: requests assignments
- Barcode demultiplexing → Barcode assignments: returns assignments