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Bowtie Summary Specifications

Process Details

  • Name: Bowtie Summary
  • Process UUID: 17fc5cd6-e169-11e9-be30-e0aab38271b1
  • Process Group: Misc.

Overview

This process parses Bowtie2 alignment output files and summarizes mapping statistics into a single consolidated report. It extracts key alignment metrics including total reads, uniquely mapped reads, and multimapped reads from multiple Bowtie2 output files and compiles them into a tab-separated values format for easy analysis and reporting.

This process is implemented in Perl.

Key Functionality

  • Bowtie2 Output Parsing: Reads and processes multiple Bowtie2 alignment output files to extract mapping statistics
  • Read Count Aggregation: Summarizes total reads, unique alignments, and multimapped reads across all input files
  • Statistical Compilation: Generates a consolidated summary table with alignment percentages and read counts
  • TSV Report Generation: Outputs results in a standardized tab-separated format for downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • Bowtie Output Files

    • Description: Set of Bowtie2 alignment output files containing mapping statistics
    • Format: bow format files

  • Sample Identifier

    • Description: Sample name or identifier for labeling the output summary
    • Format: mate format value

Outputs

  • Summary Statistics Table

    • Description: Tab-separated file containing compiled alignment statistics with columns for sample name, total reads, unique reads aligned, and multimapped reads aligned
    • Format: TSV

  • Sample Name

    • Description: The sample identifier used for output file naming and labeling
    • Format: name value

References & Resources

  • Tool Documentation: Contact the team for details on the Perl parsing script
  • 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