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Filter Host Reads Specifications

Process Details

  • Name: filter_host_reads
  • Process UUID: f93116u0w0neo0ee1wjo5r2zwjicu4
  • Process Group: Pre_Processing

Overview

This process filters out host reads from sequencing data using Bowtie2 alignment. It removes contaminating host sequences from metagenomic or transcriptomic datasets by aligning reads to a host reference genome and retaining only the unaligned (non-host) reads for downstream analysis.

This process is implemented in Bash, which invokes Bowtie2 for sequence alignment and host read removal.

Key Functionality

  • Host Read Removal: Aligns sequencing reads against a host reference genome using Bowtie2's very-sensitive alignment mode
  • Unaligned Read Recovery: Extracts and retains reads that do not align to the host genome for further analysis
  • Quality Control Logging: Generates alignment statistics and processing logs for quality assessment

Input/Output Specification

Inputs

Required Inputs

  • Reads

    • Description: Paired-end sequencing reads to be filtered for host contamination
    • Format: FASTQ

  • Bowtie2 Index

    • Description: Pre-built Bowtie2 index files for the host reference genome
    • Format: bowtie2index

Outputs

  • Reads

    • Description: Host-filtered paired-end reads that did not align to the host reference genome
    • Format: FASTQ

  • Log Output

    • Description: Bowtie2 alignment statistics and processing information including alignment rates and read counts
    • Format: out

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Bowtie2 Index
    • Description: Path to Bowtie2 index files for host genome alignment
    • Default value: ""

References & Resources

  • Tool Documentation: Contact the team for details on the Bowtie2 implementation
  • 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