hostzap

A Nextflow pipeline for host read removal from paired-end sequencing data. Given a samplesheet of FASTQ files, hostzap runs one or more host depletion tools and outputs the cleaned reads alongside summary statistics.

Tools

Tool	Method
Kraken2	k-mer classification
BBMap	Sequence alignment
Hostile	Targeted host removal
Deacon	Host sequence depletion

Each tool can be skipped individually with --skip_kraken2, --skip_bbmap, --skip_hostile, or --skip_deacon.

Usage

nextflow run main.nf \
  --input samplesheet.csv \
  --outdir results \
  --kraken2_db /path/to/kraken2_db \
  --hostile_index human-t2t-hla

The samplesheet must be a CSV with three columns:

sample-id,forward-absolute-filepath,reverse-absolute-filepath
sample1,/data/sample1_R1.fastq.gz,/data/sample1_R2.fastq.gz

Requirements

• Nextflow (DSL2)
• Docker, Singularity (conda is not tested and not recommended)