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IMG-GAP has now becoming MetaGaAP.
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# DISCLAIMER | ||
Firstly, this has only been tested and used in Ubuntu. I am not responsible for any issues or customisations that you implement or that may happen when the pipeline is used. | ||
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Don't forget to cite the pipeline and all of the software used. | ||
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# Pre-Requisites | ||
Make sure you have enough RAM otherwise it will fail at the de novo assembly step! | ||
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The pipeline requires the following software pre-installed and in your PATH: | ||
1. BWA | ||
2. SAMtools | ||
3. BEDtools | ||
4. VCFtools | ||
5. BCFtools | ||
6. bam2fastx as part of the TopHat package | ||
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The pipeline requires the following software installed/downloaded: | ||
Note: Make sure the software below are NOT in your PATH. You will specify where the software is located and the pipeline will do the rest. | ||
1. Genome Analysis Toolkit | ||
2. Kmergenie | ||
3. Tadpole as part of the BBmap package | ||
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Furthermore, the final step in this pipeline is to take your merged data-set and complete the mapping and concensus generation in Geneious. If you do not have Geneious, you can use something equivalent. Eventually I will code extra steps into the pipeline for users who do not have Geneious. | ||
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# Installation and Running | ||
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No installation needed. | ||
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To run the pipeline simple type the following: | ||
bash IMG_Assembly.sh | ||
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If you try to invoke the pipeline with sh IMG_Assembly.sh it will not work because the jumpto function will fail. |
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# DISCLAIMER | ||
Firstly, this has only been tested and used in Ubuntu. I am not responsible for any issues or customisations that you implement or that may happen when the pipeline is used. | ||
|
||
Don't forget to cite the pipeline and all of the software used. | ||
|
||
# Pre-Requisites | ||
Make sure you have enough storage for the database construction and final abundance mapping steps! | ||
|
||
The pipeline requires the following software pre-installed and in your PATH: | ||
1. BWA | ||
2. SAMtools | ||
3. BEDtools | ||
4. VCFtools | ||
5. BCFtools | ||
|
||
The pipeline requires the following software installed/downloaded: | ||
Note: Make sure the software below are NOT in your PATH. You will specify where the software is located and the pipeline will do the rest. | ||
1. Genome Analysis Toolkit | ||
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||
# Installation and Running | ||
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DO NOT INVOKE SUDO! SUDO will automatically be invoked when you begin installation and you will be required to input a password. This will be the one and only time you need to provide a password. | ||
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I do not have a work around at the moment for the installation but I am working on it. | ||
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bash Start.sh | ||
Select option 3 to install most packages - this will install packages required for all Invertebrate Microbiology Group pipelines. | ||
Once everything is installed, select MetaGaAP to start the analysis. | ||
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MetaGaAP will require you to set a working directory and you will need to respecify the IMG_pipelines directory. | ||
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If you have installed everything correctly as per the Start.sh installation option everything should work. | ||
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# Issues | ||
Please us the github issue tracker to report issues and I will work on it. Please also provide the log in the logs directory to see the options used. |
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Log files go to this directory |
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