CrossBlock

Script: crossblock.sh Type: Alias/Wrapper Redirects to: decontaminate.sh

CrossBlock is an alias for the decontaminate tool, which removes contaminants and normalizes coverage through a multi-stage pipeline implemented in jgi.DecontaminateByNormalization.

Tool Redirect

The crossblock.sh script is a simple wrapper that calls decontaminate.sh with all the same parameters and functionality.

What is CrossBlock?

CrossBlock is an alternative name for the decontaminate tool. Both scripts provide identical functionality for:

  • Sequential read processing through RenameAndMux.main() for multiplexed data merging
  • Optional k-mer-based error correction via Tadpole.main() with configurable aggressive/conservative modes
  • K-mer normalization using KmerNormalize.main() with Bloom filter prefiltering and target depth control
  • Read demultiplexing through DemuxByName.main() based on original read identifiers
  • Coverage-based mapping via BBMap.main() with configurable k-filter and ambiguous read handling
  • Scaffold filtering using FilterByCoverage.main() with minimum coverage, percent coverage, and length thresholds

Pipeline Architecture

The decontamination pipeline executes a fixed sequence of operations:

  1. Optional Raw Mapping: Maps original reads if mapRawReads=true for ratio-based filtering
  2. Read Merging: Concatenates multiple input files with standardized read identifiers
  3. Error Correction: Applies Tadpole k-mer correction (k=42 default) if ecct=true
  4. Normalization: Uses Bloom filter-based k-mer normalization (k=31, target=20, hashes=4)
  5. Demultiplexing: Separates reads back to original libraries using read ID prefixes
  6. Coverage Mapping: Maps normalized reads to reference assemblies using BBMap
  7. Filtering: Removes scaffolds below coverage thresholds (minc=3.5, minp=20%, minr=18, minl=500bp)

The pipeline leverages temporary file management with configurable deletion and parallel processing through ReadWrite.setZipThreads().

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Quick Usage

crossblock.sh reads=reads.fq ref=assembly.fa out=output_dir

This is equivalent to:

decontaminate.sh reads=reads.fq ref=assembly.fa out=output_dir

Key Parameters (Default Values)

  • minc=3.5 - Minimum average coverage to retain scaffold
  • minp=20 - Minimum percent coverage to retain scaffold
  • k=31 - K-mer length for normalization via KmerNormalize
  • target=20 - Target normalization depth
  • hashes=4 - Number of hash functions in Bloom filter
  • kfilter=55 - Minimum contiguous matches for BBMap alignment
  • ambig=random - Ambiguous read mapping mode