read-qc

Automate FASTQ quality control and adapter trimming by providing raw reads to generate cleaned, analysis-ready outputs. The skill handles quality filtering, adapter removal, and contamination screening, producing cleaned reads alongside QC reports for pre-alignment cleanup.

Screen for contamination in raw sequencing reads by running automated pre-alignment cleanup on FASTQ datasets. This generates contamination summaries that identify unwanted biological or technical contaminants, ensuring clean data for transcriptomics, whole-genome, or metagenomics workflows.

This read QC workflow supports metagenomics and transcriptomics FASTQ files, alongside whole-genome datasets. It processes raw reads across these sequencing workflows to perform quality assessment, trimming, and contamination screening, yielding consistent cleaned reads.

You can generate consistent QC reports for multiple FASTQ files through automated quality assessment and cleanup. Processing batches of raw reads yields standardized QC reports, cleaned reads, and contamination summaries, ensuring uniform data quality before downstream analysis.

You need to provide adapter sequences alongside raw FASTQ files as input for read trimming. The skill uses these sequences to perform accurate adapter removal and quality filtering, producing cleaned reads ready for downstream alignment pipelines.

Pre-alignment cleanup ensures deterministic outputs by standardizing the quality filtering, trimming, and contamination screening processes. It logs software versions for provenance tracking, guaranteeing reproducible cleaned reads and QC reports across multiple sequencing pipeline runs.