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BWA Align Specifications

Process Details

  • Name: bwa_align
  • Process UUID: t3auftscNwACrwg9LNPBnbbHQRY3K7
  • Process Group: gatk4

Overview

BWA Align performs sequence alignment of sequencing reads to a reference genome using the BWA MEM algorithm. This process is specifically configured for GATK4 compatibility, incorporating essential read group information and alignment parameters required for downstream variant calling workflows. The process handles both single-end and paired-end sequencing data and produces sorted BAM files ready for further genomic analysis.

This process is implemented in Bash, which invokes BWA MEM for alignment and samtools for BAM file processing.

Key Functionality

  • Reference Genome Alignment: Aligns sequencing reads to a reference genome using the BWA MEM algorithm with optimized parameters for accuracy and speed
  • Read Group Assignment: Automatically generates and assigns read group information essential for GATK compatibility and sample identification in downstream analyses
  • BAM File Generation: Converts aligned SAM output to sorted BAM format using samtools for efficient storage and downstream processing

Input/Output Specification

Inputs

Required Inputs

  • Sequencing Reads

    • Description: Raw sequencing data in FASTQ format containing the reads to be aligned
    • Format: FASTQ

  • Mate Information

    • Description: Specification of whether the sequencing data is single-end or paired-end
    • Format: mate

  • BWA Index

    • Description: Pre-built BWA index files for the reference genome used for alignment
    • Format: bwaindex

Outputs

  • Aligned BAM File
    • Description: Sorted BAM file containing aligned reads with read group information, ready for downstream GATK processing
    • Format: BAM

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • BWA MEM Alignment Parameters
    • Description: BWA MEM alignment parameters
    • Default value: -K 100000000 -v 3 -Y

References & Resources

  • Tool Documentation: Contact the team for details on BWA MEM alignment implementation
  • Related Papers: Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997