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Bowtie2 Specifications

Process Details

  • Name: Bowtie2
  • Process UUID: f931wxetfsi2cr3tabctqfi8skhosg
  • Process Group: Alignment

Overview

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. This process implements the Bowtie2 aligner for paired-end read alignment against reference genomes.

This process is implemented in Bash, which utilizes the Bowtie2 alignment software for high-performance sequence alignment.

Key Functionality

  • Paired-end Read Alignment: Aligns forward and reverse sequencing reads simultaneously to a reference genome using Bowtie2's efficient alignment algorithm
  • Index-based Reference Mapping: Utilizes pre-built Bowtie2 indices for fast reference genome lookup and alignment
  • Alignment Statistics Generation: Produces detailed alignment statistics and logs including sample information, input files, and alignment parameters
  • Unmapped Read Handling: Processes and outputs unmapped reads for downstream analysis or quality assessment

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Set of paired-end FASTQ files containing sequencing reads to be aligned
    • Format: FASTQ

  • Mate

    • Description: Mate pair information for paired-end sequencing data
    • Format: mate

  • Bowtie2 Index

    • Description: Pre-built Bowtie2 reference genome index files required for alignment
    • Format: bowtie2index

Outputs

  • Bow Files

    • Description: Bowtie2 alignment statistics and log files containing alignment metrics and process information
    • Format: bow

  • SAM File

    • Description: Sequence Alignment/Map format file containing aligned reads with alignment coordinates and quality scores
    • Format: SAM

  • Unmapped FASTQ

    • Description: FASTQ files containing reads that could not be aligned to the reference genome
    • Format: FASTQ

Parameters & Settings

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

  • Bowtie2 Threads

    • Description: Threads to be used by Bowtie2 short-read aligner. An integer from 1 to 8.
    • Default value: 4

  • Other Bowtie2 Parameters

    • Description: Enter other desired parameters here, other than '-x, -p, -1, -2, -S'
    • Default value: --no-unal

References & Resources

  • Tool Documentation: Bowtie2 Official Documentation
  • Related Papers: Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012;9(4):357-359. doi:10.1038/nmeth.1923