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Extract Unclassified Kraken Specifications

Process Details

  • Name: extract_unclassified_kraken
  • Process UUID: f93142ft73g34eqt7pwvonfsdypjy1
  • Process Group: short_read_taxonomy

Overview

This process extracts unclassified reads from input FASTQ files based on sequence identifiers obtained from Kraken taxonomic classification output. It enables researchers to isolate reads that were not assigned to any taxonomic classification for further analysis or quality assessment.

This process is implemented in Bash, which invokes Seqtk for sequence extraction operations.

Key Functionality

  • Sequence Extraction: Extracts specific reads from FASTQ files based on sequence identifiers
  • Unclassified Read Isolation: Filters out reads that were not taxonomically classified by Kraken
  • Batch Processing: Processes multiple FASTQ files simultaneously for efficient workflow execution

Input/Output Specification

Inputs

Required Inputs

  • reads

    • Description: Set of FASTQ files containing sequencing reads to be filtered
    • Format: FASTQ

  • OutTXTset

    • Description: Text files containing sequence identifiers of unclassified reads from Kraken output
    • Format: TXT

Outputs

  • fastq_set
    • Description: Filtered FASTQ files containing only the unclassified reads
    • Format: FASTQ

Parameters & Settings

No user-configurable parameters are available for this process.

References & Resources

  • Tool Documentation: Contact the team for details on Seqtk usage and sequence extraction methods