Appendix A: Processor Definitions

JSON Name JSON Value(s)
path Absolute path to sequencer output
platformType One of the following:
  • ILLUMINA
  • PACBIO
  • OXFORDNANOPORE
name Illumina/PacBio:
  • "default"
  • "testing"
Oxford Nanopore:
  • "promethion"
  • "minion"
  • "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: 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. Default value.
  • false: Scanner will assume run is complete if no logs are present.
PACBIO
address (required) URL of PacBio Sequencer
OXFORDNANOPORE
(no additional parameters)

Appendix B: Run JSON Fields

Field Name PacBio Illumina Oxford Nanopore
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 ✓

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

  • RS
  • RS II

Illumina

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

Oxford Nanopore

  • PromethION - as of PromethION Release 19.01.1
  • MinION - as of MinION Release 18.12

Note for Oxford Nanopore Sequencers: all sequencing output created before January 1 2017 is automatically skipped.