name	fastqc
description	Use when you need to perform quality control analysis on high-throughput sequencing data (fastq, bam, sam, or fast5 files) to identify potential problems before downstream analysis.
disable-model-invocation	true
user-invocable	true

fastqc

Inspect raw or cleaned sequencing reads before downstream analysis.
Generate per-sample QC reports for FASTQ, BAM, SAM, or FAST5 inputs.
Use it before trimming and again after trimming if you want a before/after QC comparison.
Pair it with multiqc when handling many samples.

# 1) QC two FASTQ files
fastqc -o fastqc_out sample_R1.fastq.gz sample_R2.fastq.gz

# 2) Run several files with multiple threads
fastqc -t 8 -o fastqc_out *.fastq.gz

name	fastqc
description	Use when you need to perform quality control analysis on high-throughput sequencing data (fastq, bam, sam, or fast5 files) to identify potential problems before downstream analysis.
disable-model-invocation	true
user-invocable	true

Inspect raw or cleaned sequencing reads before downstream analysis.
Generate per-sample QC reports for FASTQ, BAM, SAM, or FAST5 inputs.
Use it before trimming and again after trimming if you want a before/after QC comparison.
Pair it with multiqc when handling many samples.

# 1) QC two FASTQ files
fastqc -o fastqc_out sample_R1.fastq.gz sample_R2.fastq.gz

# 2) Run several files with multiple threads
fastqc -t 8 -o fastqc_out *.fastq.gz

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