Title:- Instructions to run GS Assembler and Mapper Course # BIOL 8803 Special Topic on Computational Genomics Assembly Group

Transcription

1 Title:- Instructions to run GS Assembler and Mapper Course # BIOL 8803 Special Topic on Computational Genomics Assembly Group

2 Contents 1. Genome Assembly Data and Projects GS De Novo Assembly Assembler GUI Interface Command Line Interface GS Reference Mapper GUI Interface Command Line Interface Instructions to run GS Assembler and Mapper Page 2

3 1. Genome Assembly 1.0. Data and Projects - Data folder for our project is /compgenomics2009/assembly/data in compgenomics server. - Read file for de novo assembly is demoreads.sff. - Read file for reference assembly is M13220.sff. - Use /compgenomics2009/assembly/projects folder to create all your assembly and mapper projects. - Project naming convention. <Group Name>-<ddmmyyyy>-<hhmmss>. Ex. ASSEMBLY GS De Novo Assembly This application generates a consensus sequence of the whole DNA sample, by assembling the reads into contigs (de novo shotgun assembly). An option allows the use of one or more sequencing Runs performed on a Paired End library (any type, or even a combination of Paired End library types) prepared from the same DNA sample, to be analyzed together with Shotgun sequencing Run(s) and help order and orient the resulting contigs into scaffolds. (Long Paired End reads do not necessarily need to be analyzed together with Shotgun reads.) The Assembler can be operated via either GUI interface or command line interface Assembler GUI Interface - Login to compgenomics server and launch the application by executing the following single command. gsassembler - The application brings up the following entry window Instructions to run GS Assembler and Mapper Page 3

4 - Start a new project by clicking on the option New Assembly Project. It pops up a window to select your project name and directory. Enter the name and location appropriately and click Ok. Instructions to run GS Assembler and Mapper Page 4

5 - Define project parameters and add read data to the project and click on the Start button on the right. - As the application processes the data observe the status on top right corner as well as at the bottom of the window. After it finishes the Alignment Results and Flowgram window will be activated. Instructions to run GS Assembler and Mapper Page 5

6 - Result Files - Alignment Results Instructions to run GS Assembler and Mapper Page 6

7 - Flowgram Instructions to run GS Assembler and Mapper Page 7

8 Command Line Interface In command line mode we can either use a single command called runassembly for the job or group of commands it in turn wraps. We the assembly group suggests to go with the second option as it give us more flexibility. Please refer to the manual GS Data Analysis Software Manual_LowRes.pdf page 112 for command details. - Initiate an assembly project. newassembly [<Project Directory Name>] Example: newassembly /compgenomics2009/assembly/projects/demogroup Though project directory name is optional, we suggest you to mention the project directory. Follow the project naming convention defined earlier in this document. Note: mention the full path of the project. Ex. /compgenomics2009/assembly/projects/demogroup Add read data to the existing project. addrun [<Project Directory Name>] [<Read Files>] Example: addrun /compgenomics2009/assembly/projects/demogroup /compgenomics2009/assembly/data/demoreads.sff - Run the project runproject [Options] [<Project Directory Name>] Example: runproject -r /compgenomics2009/assembly/projects/demogroup GS Reference Mapper This application generates the consensus DNA sequence by mapping, or alignment, of the reads to a reference sequence; as well as a list of high confidence mutations (individual bases or blocks of bases that differ between the consensus DNA sequence of the sample and the reference sequence). Mapper application can also be operated via either GUI interface or command line interface. Instructions to run GS Assembler and Mapper Page 8

9 GUI Interface - Login to compgenomics server and launch the Mapper application by a single command. gsmapper - It will bring up the following entry window. - Click on New Reference Mapper Project. It will pop up a small window as follows - Enter the project name and location and click Ok button. Instructions to run GS Assembler and Mapper Page 9

10 - It brings up the project parameter entry window. - Enter project parameters and add the read and reference files. Instructions to run GS Assembler and Mapper Page 10

11 - After entering the parameters, input and output file (s), the start button will be activated. Click on it. Instructions to run GS Assembler and Mapper Page 11

12 - Once the project is analyzed you can study the results by navigating to Result Files, Alignment Results and Flowgram tabs. Instructions to run GS Assembler and Mapper Page 12

13 Instructions to run GS Assembler and Mapper Page 13

14 Command Line Interface Similar to Assembler application the Mapper can either be launched by a single command called runmapping or group of command that it wraps. We prefer to use the second option. Please refer to the manual GS Data Analysis Software Manual_LowRes.pdf page 176 for command details. - Initiate a new Mapping project. newmapping [<Project Directory Name>] Example: newmapping /compgenomics2009/assembly/projects/demomapping Set the reference file for the project. setref [<Project Directory>] [<Reference Files>] Example: setref /compgenomics2009/assembly/projects/demomapping /compgenomics2009/assembly/data/demoreference.fasta - Add read data files to the project. addrun [<Project Directory Name>] [<Read data files>] Example: addrun /compgenomics2009/assembly/projects/demomapping /compgenomics2009/assembly/data/m12209.sff - Run the mapping project. runproject [Options] [<Project Directory Name>] Example: runproject -r /compgenomics2009/assembly/projects/demomapping Instructions to run GS Assembler and Mapper Page 14