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HISAT2 Summary Specifications

Process Details

  • Name: HISAT2 Summary
  • Process UUID: 17fc4e44-e169-11e9-be30-e0aab38271b1
  • Process Group: Misc.

Overview

This process merges HISAT2 alignment output files into a single summary table file. It aggregates alignment statistics from multiple HISAT2 runs, providing a consolidated view of read alignment metrics including total reads, multimapped reads, and uniquely aligned reads across samples.

This process is implemented in Perl.

Key Functionality

  • File Aggregation: Merges multiple HISAT2 output files into a single summary table
  • Alignment Statistics Parsing: Extracts key alignment metrics from HISAT2 log files including total reads, multimapped reads, and uniquely aligned reads
  • Summary Report Generation: Creates a TSV-formatted summary table with standardized column headers for downstream analysis

Input/Output Specification

Inputs

Required Inputs

  • Output File Set
    • Description: Collection of HISAT2 alignment summary text files to be merged
    • Format: txt

Outputs

  • Summary Table

    • Description: Consolidated TSV file containing alignment statistics from all input files with columns for Sample, Total Reads, Multimapped Reads Aligned, and Unique Reads Aligned
    • Format: tsv

  • Process Name

    • Description: Name identifier for the summary process
    • Format: name

References & Resources

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