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Introduction：

KneadData is a streamlined quality control pipeline designed specifically for metagenomic and metatranscriptomic sequencing data. It integrates Trimmomatic for adapter/quality trimming and Bowtie2 for host contamination removal into a single, reproducible workflow. Unlike generic QC tools, KneadData is optimized for microbiome studies where efficient depletion of host (e.g., human) reads is critical before downstream taxonomic or functional profiling. It supports paired-end and single-end inputs, automatically manages intermediate files, and produces comprehensive QC statistics.

Workflow Case Analysis Versions Manual Download

Input Validation: Checks FASTQ integrity and detects encoding (Phred33/64).
Trimming: Runs Trimmomatic with user-specified or default parameters to remove adapters and low-quality bases.
Host Depletion: Aligns trimmed reads against a host reference genome using Bowtie2; matching reads are discarded.
Output Generation: Writes cleaned FASTQ files (host-depleted), logs, and a summary QC table. Intermediate files are optionally retained or auto-cleaned.