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quality-reports

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Generates and interprets per-file and cross-sample QC reports from FASTQ data with FastQC, falco, and MultiQC, covering Phred quality, per-base composition, GC, duplication, overrepresented sequences, and adapter content. Use when performing initial QC on raw sequencing reads, validating preprocessing, or judging a multi-sample cohort for outliers and batch effects. For long reads use NanoPlot; for adapter/quality remediation route to adapter-trimming, quality-filtering, or fastp-workflow.

When to use

• initial QC on raw sequencing reads
• validating preprocessing
• judging a multi-sample cohort for outliers and batch effects
• per-file short-read QC
• cross-sample aggregation
• interpreting FastQC plots against assay type

When not to use

• long reads
• adapter trimming
• quality filtering
• fastp workflow
• contamination screening
• transcriptome QC on BAM
• modification of reads

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