minoTour includes a simple to use GUI to easy configuration and uploading of sequencing run data in real time into the minoTour mySQL database 1. ABSTRACT 2. Graphical User Interface 9. Availability 4. Pore Activity and Read Quality 3. Run Summaries – Read Numbers and Rates 5. Alignments to Reference Genome 7. Anytime, anywhere… minoTour: real-time data analysis for nanopore sequence data Martin Blythe, Sunir Malla, Michael Stout and Matthew Loose DeepSEQ, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH 8. Ask for a Demo @ LC2016 ! minoTour now includes a simple to use GUI to easy configuration and upload of sequencing run data into the minoTour mySQL database Other new features include batching of BWA alignments resulting in significant speed improvements minoTour is a platform for real-time monitoring, analysis and interpretation of sequence data streamed from the Oxford Nanopore minION sequencing device, including metrics describing sequence quality and also alignment to a reference genome where appropriate. minoTour comprises a Web Browser interface into a relational database of minION sequencing data captured in real-time and includes a Graphical User Interface to assist configuration of data upload. minoTour can analyse data both pre and post base calling, can remotely notify users of key events during sequencing and exploit novel sequencing features made possible for the first time by minION devices including direct control of the device in real-time; enabling ‘run until’ experiments. minoTour is open source software, freely available on all major operating system and community development is encouraged. At London Calling 2016 we will demonstrate minoTour monitoring and analysing minION sequencing and controlling the minION sequencer in real-time. A wide range of summary information about each sequencing run is available as the run is progressing, including statistics on numbers of and lengths of reads along with sequencing rates. minoTour enables nanopore activities and read quality to be monitored in real-time Users can setup Twitter alerts for important run events such as when a specific coverage level is reached minoTour can generate summary plots for mapping reads to a reference genome using reads that have been basecalled using metricore. Raw pre-basecalled reads can also be aligned using dynamic time warping of read events data against a putative reference event trace 6. Remote control of minION runs Previous sequencing runs can be stored, managed and archived, and reads viewed and exported as fasta, fastq or SAM files from minoTour’s easy to use web interface minoTour can remotely control the minION, starting and stopping runs, renaming experiments, and even monitoring channel states whilst runs are progressing Responsive web technology enables to minoTour web service to be accessed from PCs, laptops, tablets and smartphones minoTour can be downloaded from https://github.com/minoTour/minoTour A hosted minoTour service is also available at http://minotour.nottingham.ac.uk/ For access contact [email protected] See also: Real time selective sequencing using nanopore technology. Matthew Loose, Sunir Malla, Michael Stout. BioRXiv Feb 2016

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Page 1: minoTour: real-time data analysis for nanopore sequence data...minoTour includes a simple to use GUI to easy configuration and uploading of sequencing run data in real time into the

minoTour includesasimpletouseGUItoeasyconfigurationanduploadingof sequencingrundatainrealtimeintotheminoTourmySQLdatabase

1.ABSTRACT 2.GraphicalUserInterface

9.Availability

4.PoreActivityandReadQuality

3.RunSummaries– ReadNumbersandRates 5.AlignmentstoReferenceGenome

7.Anytime,anywhere…

minoTour:real-timedataanalysisfornanoporesequencedata

MartinBlythe,SunirMalla,MichaelStoutandMatthewLooseDeepSEQ,SchoolofLifeSciences,

UniversityofNottingham,Nottingham,NG72UH

8.AskforaDemo@LC2016!

minoTour nowincludes asimpletouseGUItoeasyconfiguration andupload ofsequencingrundataintotheminoTourmySQLdatabase

Othernewfeaturesinclude batchingofBWAalignmentsresultinginsignificantspeedimprovements

minoTour isaplatformforreal-timemonitoring,analysisandinterpretationofsequencedatastreamedfromtheOxford NanoporeminION sequencing device,includingmetricsdescribingsequence qualityandalsoalignmenttoareferencegenomewhereappropriate.minoTourcomprises aWebBrowserinterfaceintoarelationaldatabaseofminIONsequencing datacapturedinreal-timeandincludesaGraphicalUserInterfacetoassistconfigurationofdataupload.minoTour cananalysedatabothpreandpostbasecalling,canremotelynotifyusersofkeyeventsduringsequencing andexploitnovelsequencing featuresmadepossibleforthefirsttimebyminIONdevicesincludingdirectcontrolofthedeviceinreal-time;enabling‘rununtil’experiments.minoTourisopen sourcesoftware,freelyavailableonallmajoroperatingsystemandcommunitydevelopmentisencouraged. AtLondonCalling2016wewilldemonstrateminoTourmonitoringandanalysingminIONsequencing andcontrollingtheminIONsequencer inreal-time.

Awiderangeofsummaryinformation abouteachsequencing runisavailableastherunisprogressing,includingstatisticsonnumbersof andlengthsofreadsalongwithsequencing rates.

minoTour enablesnanoporeactivitiesandreadqualitytobemonitoredinreal-time

UserscansetupTwitteralertsforimportantruneventssuchaswhenaspecific coveragelevelisreached

minoTour cangeneratesummaryplotsformapping readstoareferencegenome usingreadsthathavebeenbasecalledusingmetricore.

Rawpre-basecalled readscanalsobealignedusingdynamictimewarpingofreadeventsdataagainstaputativereferenceeventtrace

6.RemotecontrolofminIONruns

Previoussequencing runscanbestored,managedandarchived,andreadsviewedandexportedasfasta,fastqorSAMfilesfromminoTour’s easytousewebinterface

minoTour canremotelycontroltheminION,startingandstoppingruns,renamingexperiments, andevenmonitoringchannel stateswhilstrunsareprogressing

ResponsivewebtechnologyenablestominoTourwebservicetobeaccessed fromPCs,laptops,tabletsandsmartphones

minoTour canbedownloaded fromhttps://github.com/minoTour/minoTourAhostedminoTourserviceisalsoavailableathttp://minotour.nottingham.ac.uk/[email protected]:Realtimeselectivesequencingusingnanoporetechnology.MatthewLoose,SunirMalla,MichaelStout.BioRXivFeb2016