Appendix A: Processor Definitions

JSON Name JSON Value(s)
path Absolute path to sequencer output
platformType One of the following:
  • ILLUMINA
  • PACBIO
  • OXFORDNANOPORE
  • ULTIMA
name Illumina:
  • "default"
  • "testing"
PacBio:
  • "default"
  • "v2"
  • "testing"
Oxford Nanopore:
  • "promethion"
  • "minion"
  • "testing"
 Ultima:
  • "default"
  • "testing"
timeZone Valid String ID for Java TimeZone, which is a TZ Database name. List of TZ Database names on Wikipedia
parameters Nested JSON Object:
JSON Name JSON Value(s)
ILLUMINA
checkOutput (optional)
  • true (default): Scanner will search for BCL files to verify run is complete if no logs are present. This can negatively affect processing speed over certain network filesystems.
  • false: Scanner will assume run is complete if no logs are present.
scanDragen (optional)
  • true: Scanner will attempt to parse supported DRAGEN analysis from run directory. See "Illumina DRAGEN for more information.
  • false (default): Scanner will not attempt to parse DRAGEN analysis from run directory.
PACBIO
address (required) URL of PacBio Sequencer
OXFORDNANOPORE
(no additional parameters)
ULTIMA
nexusApiAddress (required) The base URL of the Nexus API (Ex. https://example-nexus.com)
nexusApiTokenFile (required) The location of a file containing a Nexus Auth Token

Appendix B: Run JSON Fields

Field Name PacBio Illumina Oxford Nanopore Ultima
platform ✓ ✓ ✓ ✓
runAlias ✓ ✓ ✓ ✓
sequencerFolderPath ✓ ✓ ✓
sequencerName ✓ ✓ ✓ ✓
sequencerPosition ✓ ✓ ✓ ✓
containerSerialNumber ✓ ✓ ✓ ✓
containerModel ✓ ✓ ✓ ✓
laneCount ✓ ✓ ✓ ✓
healthType ✓ ✓ ✓ ✓
startDate ✓ ✓ ✓ ✓
completedDate ✓ ✓ ✓ ✓
pairedEndRun ✓ ✓ ✓ ✓
software ✓ ✓ ✓ ✓
metrics ✓ ✓ ✓ ✓
poolNames ✓
runBasesMask ✓
bclCount ✓
callCycle ✓
chemistry ✓
imgCycle ✓
indexLengths ✓
numCycles ✓
numReads ✓
poolNames ✓
readLength ✓ ✓
scoreCycle ✓
workflowType ✓
runType ✓
protocolVersion ✓
sequencingStatus ✓
analysisStatus ✓
uploadStatus ✓
expectedFlows ✓
completedFlows ✓
waferShelf ✓
analysisExpected ✓
pipelineRuns ✓

Appendix C: Sequencers Supported by Run Scanner

This is a list of sequencers for which Run Scanner is capable of processing output.

Bold items are verified to work with Run Scanner.

Italic items are under development.

Other sequencers are expected to work so long as their output is in the same format as a sequencer whose name is bolded, however they have not been tested.

If a sequencer is not included in this list, it should be assumed to be unsupported.

PacBio - "default" processor

  • RS
  • RS II

PacBio - "v2" processor

  • Revio
  • Vega

Illumina - "default" processor

  • HiSeq 1000
  • HiSeq 2000
  • HiSeq 2500
  • HiSeq X
  • MiSeq
  • NextSeq 500
  • NextSeq 550
  • NextSeq 2000
  • NovaSeq 6000
  • NovaSeq X Plus
  • iSeq
  • MiniSeq

Ultima - "default" processor

  • UG 100

Notes for Ultima Sequencers

  • Current support is in development and subject to change

Oxford Nanopore - "promethion" processor

  • PromethION - as of PromethION Release 19.01.1

Oxford Nanopore - "minion" processor

  • MinION - as of MinION Release 18.12

Notes for Oxford Nanopore Sequencers

  • All sequencing output created before January 1 2017 is automatically skipped.
  • Supports fast5 output only - pod5 format not supported.

Appendix D: Analysis Platforms Supported by Run Scanner

This is a list of on-instrument analysis platforms for which Run Scanner is capable of processing output. For more information, see Analysis Platform Support.

  • Illumina DRAGEN - as of DRAGEN 4.1.7. Analysis output created by DRAGEN versions older than 4.1.7 will be marked UNSUPPORTED.

Files Required for Parsing Analysis Data

Run Scanner parses a number of files out of the run directory in order to serve analysis data. For compatibility between versions, sometimes a number of file locations are checked for each file. Newer versions of an analysis suite may change the location of a file. If you detect that this has occured, please open a GitHub Issue detailing the situation and including the file location.

Illumina DRAGEN

BCLConvert

Let attempt be sequencer location/run directory/Analysis/attempt number/

  • attempt/Data/BCLConvert/SampleSheet.csv (the SampleSheet.csv at the root of the Analysis cannot be used due to it not updating between attempts)
  • attempt/Data/b2c_dragen_events.csv
  • One of:
  • attempt/Data/BCLConvert/fastq/Reports/fastq_list.csv
  • attempt/Data/BCLConvert/ora_fastq/Reports/fastq_list.csv
  • The fastq files in the fastq_list.csv retrieved above must exist
  • attempt/Manifest.tsv
  • One of:
  • attempt/Data/BCLConvert/fastq/Reports/Demultiplex_Stats.csv
  • attempt/Data/BCLConvert/ora_fastq/Reports/Demultiplex_Stats.csv
  • attempt/Data/Demux/Demultiplex_Stats.csv
  • attempt/Data/Secondary_Analysis_Complete.txt