Kallisto Alignment Summary Specifications
Process Details
- Name:
Kallisto Alignment Summary - Process UUID:
c9jqxmmnrSzueW5BxQAuTUx5lPe8Ri - Process Group:
Misc.
Overview
This process generates a comprehensive summary of Kallisto alignment results across multiple samples. It analyzes Kallisto output directories to extract key alignment statistics including total reads processed, pseudoaligned reads, and uniquely mapped reads for each sample, consolidating this information into a single summary table for downstream analysis and quality assessment.
This process is implemented in Perl.
Key Functionality
- Multi-sample Analysis: Automatically detects and processes all Kallisto output directories with the naming pattern
kallisto_* - Alignment Statistics Extraction: Parses Kallisto log files and run information JSON files to extract total reads, pseudoaligned reads, and uniquely mapped reads
- Summary Table Generation: Consolidates alignment statistics from all samples into a single TSV file for easy comparison and quality control
Input/Output Specification
Inputs
Required Inputs
- Output Directory
- Description: Directory containing Kallisto alignment results with subdirectories following the naming pattern
kallisto_* - Format: Directory
- Description: Directory containing Kallisto alignment results with subdirectories following the naming pattern
Outputs
- Alignment Summary Table
- Description: Tab-separated values file containing alignment statistics for all processed samples, including sample names, total reads, pseudoaligned reads, and uniquely mapped reads
- Format: TSV
Parameters & Settings
This process does not have user-configurable parameters.
References & Resources
- Tool Documentation: Contact the team for details on the Perl script implementation