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Dedup Metaphlan Specifications

Process Details

  • Name: dedup_metaphlan
  • Process UUID: f931ib8l4o7pfy5u8pspk6c04s79xm
  • Process Group: short_read_taxonomy

Overview

This process removes duplicate sequences from SAM alignment files as part of taxonomic profiling workflows. It performs deduplication by processing SAM file headers and alignment records, then converts the cleaned data to sorted and indexed BAM format for downstream analysis.

This process is implemented in Bash, which utilizes SAMtools for BAM file conversion, sorting, and indexing operations.

Key Functionality

  • Header Processing: Extracts and deduplicates SAM file headers (@HD, @SQ, @PG records) to create a clean header structure
  • Sequence Deduplication: Removes duplicate alignment records while preserving unique sequences
  • Format Conversion: Converts deduplicated SAM files to BAM format for efficient storage and processing
  • File Indexing: Generates sorted BAM files with corresponding index files for rapid data access

Input/Output Specification

Inputs

Required Inputs

  • SAM Files
    • Description: Set of SAM alignment files containing sequencing reads aligned to reference sequences
    • Format: SAM (Sequence Alignment/Map format)

Outputs

  • SAM Files

    • Description: Deduplicated SAM files with duplicate sequences removed
    • Format: SAM (Sequence Alignment/Map format)

  • BAM Directory

    • Description: Directory containing sorted and indexed BAM files generated from deduplicated SAM data
    • Format: Directory containing BAM and BAI files

Parameters & Settings

This process does not have user-configurable parameters in the Foundry UI.

References & Resources

  • Tool Documentation: Contact the team for details on SAMtools usage and deduplication methodology
  • Related Papers: Li, H., et al. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078-2079. DOI: 10.1093/bioinformatics/btp352