. The Run Folder is saved on the instrument computer and in a remote location, specified during run setup.

Figure 1 Run Folder after demultiplexing

The Run Folder has the following naming convention, with the different elements described in :

<Date>_<InstrumentSerialNumber>_<RunNumber>_<FlowCellPosition>_<FlowCellSerialNumber><RunConfigID>

Run Folder Name Element

Description

Date

Date in format YYMMDD.

InstrumentSerialNumber

Serial number of the instrument used.

RunNumber

Number of the run on the particular instrument.

FlowCellPosition

Position of the flow cell on the instrument (1 through 4)

FlowCellSerialNumber

Serial number of the flow cell used.

RunConfigID

Run configuration ID, for troubleshooting purposes.

For example, this is a valid Run Folder name:

220622_G4X1234_0057_2_FC000007A

The Run Folder contains the following sub-folders and files:

Name

Purpose

Description

demux_filtered_fastqs

Folder

Contains the FASTQ files after demutliplexing. See What Are Demultiplexed FASTQ Files?.

logs

Folder

Contains the log files for the run. See Where Are the Run Logs?.

phix_stats

Folder

Contains the PhiX statistics for the run.

thumbnails

Folder

Contains thumbnails of images of the flow cell during the run.

unfiltered_fastqs

Folder

Contains the FASTQ files with raw sequencing data before any filtering or demultiplexing. See What Are Unfiltered FASTQ Files?.

samplesheet.csv

Run parameters file

run_config.json

Run parameters file

Parameters used to start the sequencing run, including date-time stamp, flow cell ID, operator ID , read and index lengths, and instrument serial number.

run_summary.json

Metrics file

File with run summary information.

run_complete.txt

Flag file

Flag generated when all sequencing operations are complete.

transfer_complete.txt

Flag file

Flag generated when copying the files to the remote location is complete.