QA/QC Step
Processes raw FASTQ files (paired or single), provides quality plots, optional primer trimming, optional paired-end merging, and produces QIIME 2 demultiplexed artifacts plus QA summaries.
Inputs
Choose one in config_01_qaqc.yaml:
raw_fastq_path: /abs/path/to/raw_fastqs
trimmed_fastq_path: /abs/path/to/trimmed_fastqs
sample_manifest_file: 00-data/manifest_pe.csv
preexisting_fastq_qza: /abs/path/demux.qza
Set paired_end: true|false accordingly.
Manifest formats
TSV (current QIIME 2):
Paired-end:
sample-id forward-absolute-filepath reverse-absolute-filepath
sample1 /path/to/sample1_R1.fastq.gz /path/to/sample1_R2.fastq.gz
Single-end:
sample-id absolute-filepath
sample1 /path/to/sample1_R1.fastq.gz
CSV (legacy):
Paired-end:
sample-id,absolute-filepath,direction
sample1,/path/to/sample1_R1.fastq.gz,forward
sample1,/path/to/sample1_R2.fastq.gz,reverse
Single-end:
sample-id,absolute-filepath
sample1,/path/to/sample1_R1.fastq.gz
Optional trimming
to_trim: true
fwd_primer: ATCG...
rev_primer: ATCG...
discard_untrimmed: false
minimum_length: 100
Optional merging
to_merge: true
maxdiffs: 20
merge_stagger: --p-allowmergestagger
Outputs
- Demultiplexed sequences (
raw_fastq.qzaor trimmed) and summary visualizations - Stats under
[run_name]-qaqc/stats/(raw summaries, trimmed summaries, merge stats when enabled, sequence-quality drop-off report)