Output Structure

MinKNOW organises all artifacts produced during a sequencing protocol under a single base output directory chosen when the run is started.

Data pooling	Base output path pattern	Example
Disabled (default)	/data/{protocol_group_id}/{sample_id}/{protocol_start_time}_{device_id}_{flow_cell_id}_{short_protocol_run_id}/	/data/Sample_Group/Sample/20250603_1201_3E_PAA12345_e05460c6/
Enabled	/data/{protocol_group_id}/{sample_id}/	/data/Sample_Group/Sample/

The content in curly braces is replaced at sequencing run start with the value from patterns.

Missing or empty fields will use the placeholder value defined therein.

Read output

Inside the base output directory MinKNOW creates format‑specific sub‑directories:

Format	Sub‑directories
POD5	pod5/ & pod5_skip
FASTQ	fastq_pass/ & fastq_fail/
BAM	bam_pass/ & bam_fail/
.fast5 (deprecated)	fast5_pass/, fast5_fail/ & fast5_skip/

See more about specific format support.

Report & summary output

Additional sequencing artifacts are written directly to the base protocol path:

Type	Path
HTML Report	report_{flow_cell_id}_{protocol_start_time}_{short_protocol_run_id}.html
Sequencing Summary	sequencing_summary_{flow_cell_id}_{short_protocol_run_id}_{short_run_id}.txt
Output Hash File	output_hash_{flow_cell_id}_{protocol_start_time}_{short_protocol_run_id}.csv
Sample Sheet	sample_sheet_{flow_cell_id}_{protocol_start_time}_{short_protocol_run_id}.csv
Final Summary	final_summary_{flow_cell_id}_{short_protocol_run_id}_{short_run_id}.txt
Barcode Alignment Report	barcode_alignment_{flow_cell_id}_{short_protocol_run_id}_{short_run_id}.tsv
Adaptive Sampling Decisions	adaptive_sampling/AS_decisions_{flow_cell_id}_{short_protocol_run_id}_{short_run_id}.csv
Adaptive Sampling Timings	adaptive_sampling/AS_timings_{flow_cell_id}_{short_protocol_run_id}_{short_run_id}.csv

Example directory tree

This example describes a sequencing run with pooling disabled, adaptive sampling enabled, and POD5, FASTQ and BAM turned on, which has finished sequencing:

/data/Sample_Group/Sample/20250603_1201_3E_PAA12345_e05460c6/
├── pod5/
│   ├── PAA12345_dca6f6d1_d11637af_57.pod5
│   └── …
├── fastq_pass/
│   ├── PAA12345_pass_dca6f6d1_d11637af_0.fastq.gz
│   └── …
├── fastq_fail/
│   └── …
├── bam_pass/
│   ├── PAA12345_pass_dca6f6d1_d11637af_0.bam
│   └── PAA12345_pass_dca6f6d1_d11637af_0.bam.bai
├── bam_fail/
│   └── …
├── adaptive_sampling/
│   ├── AS_decisions_PAA12345_dca6f6d1_d11637af.csv
│   └── AS_timings_PAA12345_dca6f6d1_d11637af.csv
├── sequencing_summary_PAA12345_dca6f6d1_d11637af.txt
├── output_hash_PAA12345_dca6f6d1_d11637af.csv
├── sample_sheet_PAA12345_dca6f6d1_d11637af.csv
├── final_summary_PAA12345_dca6f6d1_d11637af.txt
└── barcode_alignment_PAA12345_dca6f6d1_d11637af.tsv