Manual for Demo Data

SEQUENCE Pilotmodule SeqNext

developed by

JSI medical systems GmbH JSI medical systems Corp.Tullastr. 18 One Boston Place, Suite 2600

77975 Ettenheim Boston, MA 02108GERMANY USA

phone: +49-7822/440150-0 phone: +1-617-933-7241 Fax: +49-7822/440150-20 fax: +1-617-933-7246email: mail@jsi-medisys.com email: mail-us@jsi-medisys.com

web: www.jsi-medisys.com

(for research use only)

mailto:mail@jsi-medisys.commailto:mail@jsi-medisys.dehttp://www.jsi-medisys.com/mailto:mail-us@jsi-medisys.com

Table of Contents1 Introduction to SEQUENCE Pilot SeqNext......................................................................................22 Installation of SEQUENCE Pilot.........................................................................................................23 Get your license.................................................................................................................................34 Installation of demo data....................................................................................................................35 The first login.....................................................................................................................................46 SEQUENCE Pilot screen...................................................................................................................47 Create your own user.........................................................................................................................58 Start an analysis................................................................................................................................6

8.1 Data............................................................................................................................................68.2 Start a Run..................................................................................................................................6

9 Joining loading progress and creation of orders.............................................................................810 Worklist.......................................................................................................................................... 1011 Analysis of the demo data..............................................................................................................11

11.1 Order P-454-demo..................................................................................................................1111.1.1 Sequence Screen - Left section.......................................................................................1111.1.2 Variation/Mutation table....................................................................................................1311.1.3 Base change E2 position 20.............................................................................................1411.1.4 2bp deletion E2 position 87-88.........................................................................................2011.1.5 Base change E11 position 22...........................................................................................2011.1.6 1bp deletion E11 position 622..........................................................................................2211.1.7 1bp insertion E11 position 1690.......................................................................................2311.1.8 Base change E11 position 1942.......................................................................................2411.1.9 1bp insertion E13 position -13..........................................................................................2611.1.10 Indel E14 positions 34..36..............................................................................................2811.1.11 Entries of tab distinct......................................................................................................2911.1.12 Entries of tab other.........................................................................................................3111.1.13 Entries of tab homopolymer...........................................................................................3211.1.14 Entries of tab Warning...................................................................................................3311.1.15 Result of the order P-454-demo.....................................................................................3511.1.16 Validation.......................................................................................................................3511.1.17 Printing of a report..........................................................................................................36

11.2 Order P-Illumina-demo............................................................................................................3811.3 Order P-IonTorrent-demo.......................................................................................................40

11.3.1 Quality Score filter............................................................................................................4011.3.2 Variation/Mutation table....................................................................................................4311.3.3 Base change BRCA2-E22 position-66.............................................................................4311.3.4 Base change BRCA2-E22 position -41............................................................................4411.3.5 Deletion JAK2-E14 positions 71..75.................................................................................4511.3.6 Entry of tab homopolymer................................................................................................45

12 How to analyse the orders again....................................................................................................4713 Archiving and mutation database...................................................................................................48

Manual for demo data SEQUENCE Pilot module SeqNext 1

1 Introduction to SEQUENCE Pilot SeqNextThe module SeqNext is made for bioinformatical analysis of next-generation sequencing data and iscompatible with all major platform such as Illumina (Solexa, MiSeq), Roche (454) and Ion Torrent.Chip-based Enrichments and Multiplicom MASTR assays are supported. Moreover it offers tools forconvenient copy number variation analysis and pool analysis.SeqNext uses an unique algorithm to assemble the fragmented next-generation sequencing data.The program can detect SNPs as well as insertions and deletions of any length. The user can easilyadjust settings for mosaic detection. An internal mutation database is integrated. After the analysis, adiagnostic report for each sample is received.SeqNext is a simple, easy to use desktop application including a variety of functionalities to fit theprogram to many different specific needs.

2 Installation of SEQUENCE PilotFor the installation of SEQUENCE Pilot, please do the following:

Go to our website http://www.jsi-medisys.com/free-trial-license to obtain a free trial license.Please use the link you will receive via e-mail to download our latest version of SeqPilot.Execute the downloaded file.Press [Execute] in case of an security warning.Press [Next] in the dialogue Setup Sequence Pilot.Press [Next] after reading the Sequence Pilot module information.Check the box I accept the agreement after reading the Software License Agreement andpress [Next].Press [Next] after reading the Installation Instructions.Select a destination folder, where SEQUENCE Pilot should be installed. By default this isc:\SeqPilot. Then press [Next].Note: Please make sure, that SeqPilot is not installed under C:\program files,C:\program files (x86) or in another directory with limited rights; for executing andusing SeqPilot full reading and writing rights are required. Warning: Use another folder in case you already have an existing SEQUENCE Pilotinstallation on C:\SeqPilot. Otherwise your existing installation will be overwritten!A warning appears, that updates are only free for customers with maintenance contract. Thisdoes not apply to trial licenses. Ignore this warning by pressing [OK].Select the components, which should be installed. By default all SEQUENCE Pilot modulesare selected. Then press [Next].Select the start menu folder, where the setup should place the program's shortcuts. By defaultthis is c:\SeqPilot. Then press [Next].Check the box Create a desktop icon, if a SEQUENCE Pilot icon should be placed on yourdesktop. Then press [Next].Press [Install].Press [Finish] when the SEQUENCE Pilot installation is completed.Note: SEQUENCE Pilot is available as 32 bit version and as 64 bit version. By default thedesktop icon opens the 32 bit version. To use the 64 bit version, you have to change the linkof the SEQUENCE Pilot desktop icon. Therefore go to the bin-directory of your SEQUENCEPilot installation (by default this is C:\SeqPilot\bin). Create a desktop link for the fileSeqPilot64.exe. When the new desktop icon is used, the 64 bit version starts

Manual for demo data SEQUENCE Pilot module SeqNext 2

file:///X:/Software/Module/SeqPilotfile:///X:/Software/Module/SeqPilothttp://www.jsi-medisys.com/free-trial-license

automatically. In case you do not want to use the 32 bit version any more, please delete thedefault desktop icon.

3 Get your licenseTo get your license, please do the following:

Start SEQUENCE Pilot by clicking on the desktop icon.The program stops with the message

Press [OK], to close the dialogue.Please send the JSI.cfg file as an email attachment to mail@jsi-medisys.de. It is located inthe bin-directory of the SEQUENCE Pilot