BBMap BBmerge Specifications

Process Details

• Name: BBMap BBmerge
• Process UUID: 8c211071cd584e58aaef5987f9cf7c7f
• Process Group: Misc.

Overview

BBMap BBmerge is a specialized module from the BBMap suite designed to merge paired-end FASTQ reads. This process combines forward and reverse FASTQ files, producing merged reads where the paired sequences overlap sufficiently, while preserving unmerged reads separately. The tool is particularly useful for preprocessing paired-end sequencing data where read overlap can improve downstream analysis quality.

This process is implemented in Bash, utilizing the bbmerge.sh tool from the BBMap package (version 39.28).

Key Functionality

• Paired-end Read Merging: Combines overlapping forward and reverse reads into single merged sequences
• Flexible Input Format Support: Processes both compressed (.gz) and uncompressed FASTQ files
• Unmerged Read Preservation: Maintains separate output files for reads that cannot be merged
• Quality-based Merging: Uses sequence quality scores to optimize merge decisions

Input/Output Specification

Inputs

Required Inputs

• mate

  • Description: Mate pair specification indicating paired-end sequencing data
  • Format: Configuration parameter (must be "pair")

• reads

  • Description: Set of paired FASTQ files containing forward and reverse sequencing reads
  • Format: FASTQ files (compressed or uncompressed)

Outputs

• reads
  • Description: Processed FASTQ files including merged reads and separated unmerged forward/reverse reads
  • Format: FASTQ files (compressed .gz format)

Parameters & Settings

This process operates with fixed parameters optimized for standard paired-end read merging. The merging behavior is controlled by BBmerge's default quality and overlap thresholds.

References & Resources

• Tool Documentation: Contact the team for details on bbmerge.sh
• Related Papers: Bushnell, B. (2014). BBMap: A Fast, Accurate, Splice-Aware Aligner. Lawrence Berkeley National Laboratory. LBNL-7065E.