LIMS Integration for Illumina Novaseq

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: [login to view URL] [login to view URL] [login to view URL] NOTE: Attempts to read the files is only to be done after the file “[login to view URL]” 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: [login to view URL] <?xml version="1.0" encoding="utf-8"?> <RunCompletionStatus xmlns:xsi="[login to view URL]" xmlns:xsd="[login to view URL]"> <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> [login to view URL] <?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> [login to view URL] <?xml version="1.0" encoding="utf-8"?> <RunParameters xmlns:xsi="[login to view URL]" xmlns:xsd="[login to view URL]"> <Side>A</Side> <Application>NovaSeqXSeries Control Software</Application> <SystemSuiteVersion>1.3.0.39308</SystemSuiteVersion> <OutputFolder>[login to view URL]:/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>

Project ID: 40547036