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Extract Unclassified Names Specifications

Process Details

  • Name: extract_unclassified_names
  • Process UUID: f931r0lv3usuci04sfxvkb2abgdwaw
  • Process Group: short_read_taxonomy

Overview

This process extracts the names of unclassified reads from Kraken taxonomic classification output. It processes TSV files containing Kraken results to identify and extract reads that could not be taxonomically classified, generating a text file containing the names of these unclassified sequences.

This process is implemented in Bash, which invokes a Python script for extracting unclassified read names from Kraken output.

Key Functionality

  • Unclassified Read Extraction: Parses Kraken output files to identify reads that were not assigned to any taxonomic classification
  • Name Collection: Extracts and compiles the sequence identifiers of unclassified reads
  • Output Organization: Creates organized directory structure and generates text files containing unclassified read names

Input/Output Specification

Inputs

Required Inputs

  • outputFileTSV
    • Description: Kraken taxonomic classification output in TSV format containing classified and unclassified reads
    • Format: TSV

Outputs

  • OutTXTset
    • Description: Text file containing the names/identifiers of reads that could not be taxonomically classified by Kraken
    • Format: TXT

Parameters & Settings

No user-configurable parameters are available for this process.

References & Resources

  • Tool Documentation: Contact the team for details on extract_unclassified_names.py