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Build Bowtie2 Index Specifications

Process Details

  • Name: Build Bowtie2 Index
  • Process UUID: f931y13mkez48ug08zxy0z9ro8dafd
  • Process Group: Index

Overview

This process builds a Bowtie2 index from a genome FASTA file, which is essential for performing fast and accurate sequence alignments in downstream RNA-seq, ChIP-seq, ATAC-seq, and other sequencing analyses. The Bowtie2 index is a compressed representation of the reference genome that enables efficient read mapping.

This process is implemented in Bash, utilizing the Bowtie2 alignment tool for index construction.

Key Functionality

  • Index Construction: Builds a Bowtie2 index from input FASTA files using the bowtie2-build command
  • File Processing: Handles compressed (.gz) FASTA files by automatically decompressing them during processing
  • Multi-threading Support: Utilizes available CPU cores to accelerate index building process
  • Flexible Naming: Automatically processes file names and creates appropriately named index files

Input/Output Specification

Inputs

Required Inputs

  • FASTA File
    • Description: Reference genome sequence in FASTA format
    • Format: FASTA (.fasta, .fa, .FA)

Outputs

  • Bowtie2 Index

    • Description: Complete Bowtie2 index files for the reference genome
    • Format: Bowtie2 index format (.bt2 files)

  • Log Output

    • Description: Process execution log containing build statistics and file information
    • Format: Text log file (.out)

Parameters & Settings

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

  • Other index builder parameters
    • Description: Enter other desired Bowtie2 index building parameters here. Other than '--threads'. e.g. '--large-index --seed 123'
    • Default value: "" (empty)

References & Resources

  • Tool Documentation: Bowtie2 Manual
  • Related Papers: Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357–359 (2012). https://doi.org/10.1038/nmeth.1923