FASTQ QC

Use this skill for QC-only, trimming-first, or FASTQ quality interpretation workflows. This skill can execute the plugin-owned local FastQ QC runner when the user approves a local run. It should decide whether trimming or additional investigation is warranted; it should not blindly trim by default.

Essential Inputs

Confirm:

• FASTQ paths and pairing convention
• whether output should be QC-only or trimmed FASTQs
• known adapter or primer sequences
• organism if contamination screening or host depletion is requested
• output directory
• whether FASTQs are raw, demultiplexed, previously trimmed, or downloaded from an archive
• whether downstream analysis expects original read lengths, UMIs, or inline barcodes

Public Tools

Default tool set: