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Check Build Bowtie2 Index Specifications

Process Details

  • Name: Check Build Bowtie2 Index
  • Process UUID: 17fc7964-e169-11e9-be30-e0aab38271b1
  • Process Group: Index

Overview

This process builds a Bowtie2 index from a genome FASTA file for use in RNA-seq and DNA-seq alignment workflows. The process intelligently checks if a Bowtie2 index already exists for the given genome and only builds a new index if necessary. If an index exists, it creates a symbolic link to the existing index directory to avoid redundant computation.

This process is implemented in Bash, which invokes the Bowtie2 indexing tool for genome index construction.

Key Functionality

  • Index Validation: Checks for the existence of Bowtie2 index files before attempting to build
  • Conditional Index Building: Creates a new Bowtie2 index only when required files are missing
  • Directory Management: Sets up proper directory structure and symbolic links for index organization
  • Resource Optimization: Avoids redundant index building by reusing existing compatible indices

Input/Output Specification

Inputs

Required Inputs

  • Genome
    • Description: Reference genome sequence in FASTA format used for building the Bowtie2 index
    • Format: FASTA

Outputs

  • Bowtie2 Index
    • Description: Complete Bowtie2 index files ready for use in alignment processes
    • Format: bowtie2index

Parameters & Settings

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

  • Bowtie2 Build Parameters
    • Description: Bowtie2 build parameters
    • Default value: --threads 5

References & Resources

  • Tool Documentation: Contact the team for details on the Bowtie2 indexing implementation
  • Related Papers: Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359. DOI: 10.1038/nmeth.1923