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}/{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.

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}_{daq_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}_{daq_start_time}_{short_protocol_run_id}.csv
Sample Sheet	sample_sheet_{flow_cell_id}_{daq_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