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FileStructure.rst

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Revio file structure

The Revio platform has a different output file structure than Sequel II and Sequel IIe.

Directory structure

Transfer_Scheme_Path/
└─ rNNNNN_YYYYMMDD_HHMMSS/
   └─ P_WNN/
      ├─ fail_reads/
      ├─ hifi_reads/
      ├─ metadata/
      ├─ pb_formats/
      └─ statistics/

Movie Context ID is defined as

mNNNNN_YYMMDD_HHMMSS_sN

in particular:

mNNNNN - instrument identifier
YYMMDD - date stamp
HHMMSS - time stamp
sN     - stage number (Revio has four)

File structure

In the following example, one barcode ('bc2001') has been used. If you see the 'default' file infix, this is the standard, unbarcoded TC6 SMRTbell adapter.

Transfer_Scheme_Path/
└─r84001_20220722_134701
  └─1_A01
    ├─ fail_reads
    │  ├─ m84001_220722_134701_s1.fail_reads.bc2001.bam
    │  ├─ m84001_220722_134701_s1.fail_reads.bc2001.bam.pbi
    │  ├─ m84001_220722_134701_s1.fail_reads.unassigned.bam
    │  └─ m84001_220722_134701_s1.fail_reads.unassigned.bam.pbi
    ├─ hifi_reads
    │  ├─ m84001_220722_134701_s1.hifi_reads.bc2001.bam
    │  ├─ m84001_220722_134701_s1.hifi_reads.bc2001.bam.pbi
    │  ├─ m84001_220722_134701_s1.hifi_reads.unassigned.bam
    │  └─ m84001_220722_134701_s1.hifi_reads.unassigned.bam.pbi
    ├─ metadata
    │  ├─ m84001_220722_134701_s1.barcodes.fasta
    │  ├─ m84001_220722_134701_s1.basecaller.log
    │  ├─ m84001_220722_134701_s1.ccs.log
    │  ├─ m84001_220722_134701_s1.darkcal.log
    │  ├─ m84001_220722_134701_s1.fail_reads.alarms.json
    │  ├─ m84001_220722_134701_s1.fail_reads.lima.log
    │  ├─ m84001_220722_134701_s1.fail_reads.primrose.log
    │  ├─ m84001_220722_134701_s1.hifi_reads.alarms.json
    │  ├─ m84001_220722_134701_s1.hifi_reads.lima.log
    │  ├─ m84001_220722_134701_s1.hifi_reads.primrose.log
    │  ├─ m84001_220722_134701_s1.metadata.xml
    │  ├─ m84001_220722_134701_s1.ppa.log
    │  ├─ m84001_220722_134701_s1.run.metadata.xml
    │  ├─ m84001_220722_134701_s1.sts.xml
    │  └─ m84001_220722_134701_s1.transferdone
    ├─ pb_formats
    │  ├─ m84001_220722_134701_s1.consensusreadset.xml
    │  ├─ m84001_220722_134701_s1.fail_reads.bc2001.consensusreadset.xml
    │  ├─ m84001_220722_134701_s1.fail_reads.consensusreadset.xml
    │  ├─ m84001_220722_134701_s1.fail_reads.unassigned.consensusreadset.xml
    │  ├─ m84001_220722_134701_s1.hifi_reads.bc2001.consensusreadset.xml
    │  ├─ m84001_220722_134701_s1.hifi_reads.consensusreadset.xml
    │  └─ m84001_220722_134701_s1.hifi_reads.unassigned.consensusreadset.xml
    └─ statistics
       ├─ m84001_220722_134701_s1.ccs_reports.json
       ├─ m84001_220722_134701_s1.fail_reads.5mc_report.json
       ├─ m84001_220722_134701_s1.fail_reads.lima_counts.txt
       ├─ m84001_220722_134701_s1.fail_reads.lima_guess.json
       ├─ m84001_220722_134701_s1.fail_reads.lima_report.txt
       ├─ m84001_220722_134701_s1.fail_reads.lima_summary.txt
       ├─ m84001_220722_134701_s1.hifi_reads.5mc_report.json
       ├─ m84001_220722_134701_s1.hifi_reads.lima_counts.txt
       ├─ m84001_220722_134701_s1.hifi_reads.lima_guess.json
       ├─ m84001_220722_134701_s1.hifi_reads.lima_report.txt
       ├─ m84001_220722_134701_s1.hifi_reads.lima_summary.txt
       └─ m84001_220722_134701_s1.zmw_metrics.json.gz