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Check Build BWA Specifications

Process Details

  • Name: Check_Build_BWA
  • Process UUID: NbMbUHbingbHxx9zk26qhpC7HQzN5i
  • Process Group: Index

Overview

This process builds a BWA index using a genome FASTA file for sequence alignment applications. The process checks if the index exists, and if not, creates it and sets up a symbolic link to the index directory. This is an essential preprocessing step for BWA-based genomic alignment workflows.

This process is implemented in Bash, which invokes BWA, Samtools, and GATK tools for comprehensive genome indexing.

Key Functionality

  • BWA Index Creation: Builds BWA index files from the input genome FASTA file using the BWA indexing algorithm
  • FASTA Index Generation: Creates a FASTA index (.fai) file using Samtools for rapid sequence retrieval
  • Sequence Dictionary Creation: Generates a sequence dictionary file using GATK for compatibility with downstream GATK tools

Input/Output Specification

Inputs

Required Inputs

  • Genome
    • Description: Reference genome sequence in FASTA format
    • Format: FASTA

Outputs

  • BWA Index
    • Description: Complete BWA index package containing all necessary index files for BWA alignment
    • Format: BWAIndex

Parameters & Settings

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

  • BWA Build Parameters
    • Description: BWA build parameters
    • Default value: "" (empty string)

References & Resources

  • Tool Documentation: Contact the team for details on BWA, Samtools, and GATK integration scripts
  • Related Papers: Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. doi:10.1093/bioinformatics/btp324