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Map Bowtie2 Specifications

Process Details

  • Name: Map Bowtie2
  • Process UUID: 20bdb1d4-ed05-11e8-9ce4-85221b21564c
  • Process Group: Alignment

Overview

Map Bowtie2 is an ultrafast and memory-efficient alignment process for mapping sequencing reads to long reference sequences. It is particularly effective at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long genomes, such as mammalian genomes. This process handles both single-end and paired-end sequencing data and produces high-quality alignments in standard bioinformatics formats.

This process is implemented in Bash, which utilizes Bowtie2 for sequence alignment and SAMtools for file format conversion.

Key Functionality

  • Sequence Alignment: Maps sequencing reads to reference genomes using the Bowtie2 algorithm with optimized parameters for speed and accuracy
  • Paired-End Support: Automatically detects and processes both single-end and paired-end sequencing data
  • Output Format Conversion: Converts alignment results from SAM to BAM format for downstream analysis compatibility
  • Quality Filtering: Excludes unmapped reads and filters warning messages from alignment output

Input/Output Specification

Inputs

Required Inputs

  • Sequencing Reads

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

  • Mate Information

    • Description: Specification of whether the data is single-end or paired-end sequencing
    • Format: Mate designation (single/pair)

  • Bowtie2 Index

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

Outputs

  • Alignment Files

    • Description: Bowtie2 alignment output files containing mapping statistics and alignment information
    • Format: BOW

  • Unmapped Reads

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

  • Binary Alignment Files

    • Description: Compressed binary alignment files suitable for downstream analysis and visualization
    • Format: BAM

Parameters & Settings

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

  • Bowtie2 Parameters
    • Description: Bowtie2 parameters
    • Default value: -p 3

References & Resources

  • Tool Documentation: Contact the team for details on Map_Bowtie2
  • Related Papers: Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357-359. DOI: 10.1038/nmeth.1923