LIMS Integration for Illumina Novaseq
Budget: $250 – $750 AUD
Solution MUST use SampleManager's Integration Manager. This is not a software development project.
Need a ThermoFisher Sample Manager LIMS Integration Manager expert to build an integration to support the import of metadata from an Illumina Novaseq sequencer into a SampleManager LIMS analysis.
The integration and analysis needs to be built on the freelancers system and supplied as SQL to allow the update of the local SampleManager LIMS instance. If this is not considered viable way to transfer the results then the freelancer needs to suggest a methodology to configure this integration and analysis into the client LIMS system.
The Illumina results will be found in folders under the following folder name:
X:\Illumina\Data_Output\
And will be in a folder named like:
20260218_LH01013_0001_A2373TFLT4
Where the folder name is made up from;
Run Date: 20260218
Instrument: LH01013
Sample number: 0001
Flowcell: A2373TFLT4
And the files to be read from this folder are:
RunCompletionStatus.xml
RunInfo.xml
RunParameters.xml
NOTE: Attempts to read the files is only to be done after the file “CopyComplete.txt” has been written to the X:\Illumina\Data_Output\20260218_LH01013_0001_A2373TFLT4 folder.
NOTE: the folder name supplied here is an example of the format to be expected only. It will be different for every run and the integration needs to take this into account to extract the sample number for example.
The required components of the Analysis:
RunCompletionStatus
RunStartTime - date
RunEndTime - date
PreRunChecksDuration - duration hours
PostRunWashDuration - duration hours
PostRunProtocolDuration - duration hours
TotalRunTime duration - days and hours
Foreach CompletedReads
ReadName - test
Cycles - integer
RunStatus - test
RunInfo
RunInfoVersion - integer
RunId - text
RunIDNumber - integer
Flowcell - text
Instrument - text
RunDate - date
Foreach Read
ReadNumber - integer
ReadNumCycles - integer
ReadIsIndexedRead - char(1)
ReadIsReverseComplement - char(1)
FlowcellLayoutLaneCount - integer
FlowcellLayoutSurfaceCount - integer
FlowcellLayoutSwathCount - integer
FlowcellLayoutTileCount - integer
TileSetTileNamingConvention - text
ImageDimensionsWidth - integer
ImageDimensionsHeight - integer
Foreach ImageChannels
Name - text
RunParameters
Side - char(1)
Application - text
SystemSuiteVersion - text
OutputFolder - text
ReadOnePrimer - boolean
ReadTwoPrimer - boolean
IndexOnePrimer - boolean
IndexTwoPrimer - boolean
CloudUploadMode - text
RunSetupMode - text
SecondaryAnalysisMode - text
InstrumentType - text
InstrumentSerialNumber - text
RunId - text
FlowCellName - text
FlowCellType - text
Foreach ConsumableInfo
SerialNumber - text
LotNumber - text
PartNumber - text
ExpirationDate - date
Type - text
Mode - integer
Version - float
Name - text
Foreach PlannedReads
PlannedReadReadName - text
PlannedReadCycles - integer
DisableBclCopy - boolean
RunCounter - integer
RecipeName - text
RecipeVersion - text
ExperimentName - text
The contents of the files to read:
RunCompletionStatus.xml
<?xml version="1.0" encoding="utf-8"?>
<RunCompletionStatus xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<RunStartTime>2026-02-18T14:34:22.6387261+04:00</RunStartTime>
<RunEndTime>2026-02-20T10:04:25.4234506+04:00</RunEndTime>
<PreRunChecksDuration>00:27:16.2959254</PreRunChecksDuration>
<PostRunWashDuration>01:47:45.6631511</PostRunWashDuration>
<PostRunProtocolDuration>00:02:58.0248658</PostRunProtocolDuration>
<TotalRunTime>1.19:30:02.7847245</TotalRunTime>
<CompletedReads>
<Read ReadName="Read1" Cycles="151" />
<Read ReadName="Read2" Cycles="151" />
</CompletedReads>
<RunStatus>RunCompleted</RunStatus>
</RunCompletionStatus>
RunInfo.xml
<?xml version="1.0"?>
<RunInfo Version="6">
<Run Id="20260218_LH01013_0001_A2373TFLT4" Number="1">
<Flowcell>2373TFLT4</Flowcell>
<Instrument>LH01013</Instrument>
<Date>2026-02-18T16:43:54Z</Date>
<Reads>
<Read Number="1" NumCycles="151" IsIndexedRead="N" IsReverseComplement="N"/>
<Read Number="2" NumCycles="151" IsIndexedRead="N" IsReverseComplement="N"/>
</Reads>
<FlowcellLayout LaneCount="8" SurfaceCount="2" SwathCount="4" TileCount="98">
<TileSet TileNamingConvention="FourDigit">
</TileSet>
</FlowcellLayout>
<ImageDimensions Width="5120" Height="2879"/>
<ImageChannels>
<Name>blue</Name>
<Name>green</Name>
</ImageChannels>
</Run>
</RunInfo>
RunParameters.xml
<?xml version="1.0" encoding="utf-8"?>
<RunParameters xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<Side>A</Side>
<Application>NovaSeqXSeries Control Software</Application>
<SystemSuiteVersion>1.3.0.39308</SystemSuiteVersion>
<OutputFolder>10.183.31.14:/Laboratory/Illumina/Data_Output/20260218_LH01013_0001_A2373TFLT4</OutputFolder>
<CustomPrimerSelections>
<ReadOnePrimer>false</ReadOnePrimer>
<ReadTwoPrimer>false</ReadTwoPrimer>
<IndexOnePrimer>false</IndexOnePrimer>
<IndexTwoPrimer>false</IndexTwoPrimer>
</CustomPrimerSelections>
<CloudUploadMode>InstrumentPerformance</CloudUploadMode>
<RunSetupMode>Manual</RunSetupMode>
<SecondaryAnalysisMode>None</SecondaryAnalysisMode>
<InstrumentType>NovaSeqXPlus</InstrumentType>
<InstrumentSerialNumber>LH01013</InstrumentSerialNumber>
<RunId>20260218_LH01013_0001_A2373TFLT4</RunId>
<FlowCellName>NovaSeqXSeries B4</FlowCellName>
<FlowCellType>NovaSeqXSeriesB4</FlowCellType>
<ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC1157697-LS1</SerialNumber>
<LotNumber>1000029809</LotNumber>
<PartNumber>20101913</PartNumber>
<ExpirationDate>2027-09-14T00:00:00+04:00</ExpirationDate>
<Type>SampleTube</Type>
<Mode>3</Mode>
<Version>1.0</Version>
<Name>8 Lane</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC4502642-25B3</SerialNumber>
<LotNumber>21009819</LotNumber>
<PartNumber>20066626</PartNumber>
<ExpirationDate>2027-05-25T00:00:00+04:00</ExpirationDate>
<Type>Reagent</Type>
<Mode>4</Mode>
<Version>1.5</Version>
<Name>25B 300c</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC2310652-LI6</SerialNumber>
<LotNumber>18407736</LotNumber>
<PartNumber>20090671</PartNumber>
<ExpirationDate>2027-04-17T00:00:00+04:00</ExpirationDate>
<Type>Lyo</Type>
<Mode>11</Mode>
<Version>1.5</Version>
<Name>High</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>BC1100004471-1</SerialNumber>
<LotNumber>20982416</LotNumber>
<PartNumber>20089853</PartNumber>
<ExpirationDate>2027-03-19T00:00:00+04:00</ExpirationDate>
<Type>Buffer</Type>
<Mode>3</Mode>
<Version>1.0</Version>
<Name>Universal</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>2373TFLT4</SerialNumber>
<LotNumber>20977451</LotNumber>
<PartNumber>20088039</PartNumber>
<ExpirationDate>2027-01-21T00:00:00+04:00</ExpirationDate>
<Type>FlowCell</Type>
<Mode>4</Mode>
<Version>1.0</Version>
<Name>25B</Name>
</ConsumableInfo>
</ConsumableInfo>
<PlannedReads>
<Read ReadName="Read1" Cycles="151" />
<Read ReadName="Read2" Cycles="151" />
</PlannedReads>
<SecondaryAnalysisInfo />
<DisableBclCopy>false</DisableBclCopy>
<RunCounter>1</RunCounter>
<RecipeName>25B Sequencing</RecipeName>
<RecipeVersion>25B-01.03.03</RecipeVersion>
<ExperimentName>Validation SideA</ExperimentName>
</RunParameters>
Need a ThermoFisher Sample Manager LIMS Integration Manager expert to build an integration to support the import of metadata from an Illumina Novaseq sequencer into a SampleManager LIMS analysis.
The integration and analysis needs to be built on the freelancers system and supplied as SQL to allow the update of the local SampleManager LIMS instance. If this is not considered viable way to transfer the results then the freelancer needs to suggest a methodology to configure this integration and analysis into the client LIMS system.
The Illumina results will be found in folders under the following folder name:
X:\Illumina\Data_Output\
And will be in a folder named like:
20260218_LH01013_0001_A2373TFLT4
Where the folder name is made up from;
Run Date: 20260218
Instrument: LH01013
Sample number: 0001
Flowcell: A2373TFLT4
And the files to be read from this folder are:
RunCompletionStatus.xml
RunInfo.xml
RunParameters.xml
NOTE: Attempts to read the files is only to be done after the file “CopyComplete.txt” has been written to the X:\Illumina\Data_Output\20260218_LH01013_0001_A2373TFLT4 folder.
NOTE: the folder name supplied here is an example of the format to be expected only. It will be different for every run and the integration needs to take this into account to extract the sample number for example.
The required components of the Analysis:
RunCompletionStatus
RunStartTime - date
RunEndTime - date
PreRunChecksDuration - duration hours
PostRunWashDuration - duration hours
PostRunProtocolDuration - duration hours
TotalRunTime duration - days and hours
Foreach CompletedReads
ReadName - test
Cycles - integer
RunStatus - test
RunInfo
RunInfoVersion - integer
RunId - text
RunIDNumber - integer
Flowcell - text
Instrument - text
RunDate - date
Foreach Read
ReadNumber - integer
ReadNumCycles - integer
ReadIsIndexedRead - char(1)
ReadIsReverseComplement - char(1)
FlowcellLayoutLaneCount - integer
FlowcellLayoutSurfaceCount - integer
FlowcellLayoutSwathCount - integer
FlowcellLayoutTileCount - integer
TileSetTileNamingConvention - text
ImageDimensionsWidth - integer
ImageDimensionsHeight - integer
Foreach ImageChannels
Name - text
RunParameters
Side - char(1)
Application - text
SystemSuiteVersion - text
OutputFolder - text
ReadOnePrimer - boolean
ReadTwoPrimer - boolean
IndexOnePrimer - boolean
IndexTwoPrimer - boolean
CloudUploadMode - text
RunSetupMode - text
SecondaryAnalysisMode - text
InstrumentType - text
InstrumentSerialNumber - text
RunId - text
FlowCellName - text
FlowCellType - text
Foreach ConsumableInfo
SerialNumber - text
LotNumber - text
PartNumber - text
ExpirationDate - date
Type - text
Mode - integer
Version - float
Name - text
Foreach PlannedReads
PlannedReadReadName - text
PlannedReadCycles - integer
DisableBclCopy - boolean
RunCounter - integer
RecipeName - text
RecipeVersion - text
ExperimentName - text
The contents of the files to read:
RunCompletionStatus.xml
<?xml version="1.0" encoding="utf-8"?>
<RunCompletionStatus xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<RunStartTime>2026-02-18T14:34:22.6387261+04:00</RunStartTime>
<RunEndTime>2026-02-20T10:04:25.4234506+04:00</RunEndTime>
<PreRunChecksDuration>00:27:16.2959254</PreRunChecksDuration>
<PostRunWashDuration>01:47:45.6631511</PostRunWashDuration>
<PostRunProtocolDuration>00:02:58.0248658</PostRunProtocolDuration>
<TotalRunTime>1.19:30:02.7847245</TotalRunTime>
<CompletedReads>
<Read ReadName="Read1" Cycles="151" />
<Read ReadName="Read2" Cycles="151" />
</CompletedReads>
<RunStatus>RunCompleted</RunStatus>
</RunCompletionStatus>
RunInfo.xml
<?xml version="1.0"?>
<RunInfo Version="6">
<Run Id="20260218_LH01013_0001_A2373TFLT4" Number="1">
<Flowcell>2373TFLT4</Flowcell>
<Instrument>LH01013</Instrument>
<Date>2026-02-18T16:43:54Z</Date>
<Reads>
<Read Number="1" NumCycles="151" IsIndexedRead="N" IsReverseComplement="N"/>
<Read Number="2" NumCycles="151" IsIndexedRead="N" IsReverseComplement="N"/>
</Reads>
<FlowcellLayout LaneCount="8" SurfaceCount="2" SwathCount="4" TileCount="98">
<TileSet TileNamingConvention="FourDigit">
</TileSet>
</FlowcellLayout>
<ImageDimensions Width="5120" Height="2879"/>
<ImageChannels>
<Name>blue</Name>
<Name>green</Name>
</ImageChannels>
</Run>
</RunInfo>
RunParameters.xml
<?xml version="1.0" encoding="utf-8"?>
<RunParameters xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
<Side>A</Side>
<Application>NovaSeqXSeries Control Software</Application>
<SystemSuiteVersion>1.3.0.39308</SystemSuiteVersion>
<OutputFolder>10.183.31.14:/Laboratory/Illumina/Data_Output/20260218_LH01013_0001_A2373TFLT4</OutputFolder>
<CustomPrimerSelections>
<ReadOnePrimer>false</ReadOnePrimer>
<ReadTwoPrimer>false</ReadTwoPrimer>
<IndexOnePrimer>false</IndexOnePrimer>
<IndexTwoPrimer>false</IndexTwoPrimer>
</CustomPrimerSelections>
<CloudUploadMode>InstrumentPerformance</CloudUploadMode>
<RunSetupMode>Manual</RunSetupMode>
<SecondaryAnalysisMode>None</SecondaryAnalysisMode>
<InstrumentType>NovaSeqXPlus</InstrumentType>
<InstrumentSerialNumber>LH01013</InstrumentSerialNumber>
<RunId>20260218_LH01013_0001_A2373TFLT4</RunId>
<FlowCellName>NovaSeqXSeries B4</FlowCellName>
<FlowCellType>NovaSeqXSeriesB4</FlowCellType>
<ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC1157697-LS1</SerialNumber>
<LotNumber>1000029809</LotNumber>
<PartNumber>20101913</PartNumber>
<ExpirationDate>2027-09-14T00:00:00+04:00</ExpirationDate>
<Type>SampleTube</Type>
<Mode>3</Mode>
<Version>1.0</Version>
<Name>8 Lane</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC4502642-25B3</SerialNumber>
<LotNumber>21009819</LotNumber>
<PartNumber>20066626</PartNumber>
<ExpirationDate>2027-05-25T00:00:00+04:00</ExpirationDate>
<Type>Reagent</Type>
<Mode>4</Mode>
<Version>1.5</Version>
<Name>25B 300c</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>LC2310652-LI6</SerialNumber>
<LotNumber>18407736</LotNumber>
<PartNumber>20090671</PartNumber>
<ExpirationDate>2027-04-17T00:00:00+04:00</ExpirationDate>
<Type>Lyo</Type>
<Mode>11</Mode>
<Version>1.5</Version>
<Name>High</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>BC1100004471-1</SerialNumber>
<LotNumber>20982416</LotNumber>
<PartNumber>20089853</PartNumber>
<ExpirationDate>2027-03-19T00:00:00+04:00</ExpirationDate>
<Type>Buffer</Type>
<Mode>3</Mode>
<Version>1.0</Version>
<Name>Universal</Name>
</ConsumableInfo>
<ConsumableInfo>
<SerialNumber>2373TFLT4</SerialNumber>
<LotNumber>20977451</LotNumber>
<PartNumber>20088039</PartNumber>
<ExpirationDate>2027-01-21T00:00:00+04:00</ExpirationDate>
<Type>FlowCell</Type>
<Mode>4</Mode>
<Version>1.0</Version>
<Name>25B</Name>
</ConsumableInfo>
</ConsumableInfo>
<PlannedReads>
<Read ReadName="Read1" Cycles="151" />
<Read ReadName="Read2" Cycles="151" />
</PlannedReads>
<SecondaryAnalysisInfo />
<DisableBclCopy>false</DisableBclCopy>
<RunCounter>1</RunCounter>
<RecipeName>25B Sequencing</RecipeName>
<RecipeVersion>25B-01.03.03</RecipeVersion>
<ExperimentName>Validation SideA</ExperimentName>
</RunParameters>