AMI Usage

Connecting to the instance

After launching the instance using AWS Interface, you can connect to the instance using ssh with username centos and your key file

ssh -i <location_of_your_pem_file> centos@<instance_ip>

Software Included

Inside the AMI all the necessary software to run Hugenomic Nanopolish is already installed. You can directly launch the executable as

hug-nanopolish

The binary takes care of setting up the environment and starting the computation. For your convenience, inside the instance you will find the executables to launch minimap2 (same version as the one pointed by Nanopolis v0.13.2). The location of minimap2 binary is

/huxelerate/hugenomic/

Regarding possible parameters, please refer to nanopolish documentation for the complete options provided by this tool.

Note

The default number of threads for module eventalign is 12 and it is optimized to be used on the f1.2xlarge instance. It is however possible to overload the number of threads by using the -t option.

Note

When using the eventalign module with –samples, the output produced can be massive. To improve the performance of the AMI, it is suggested to use two different volumes, one for reading the inputs and one for storing the outputs of the computation.

Example usage

hug-nanopolish eventalign \
--reads reads.fasta \
--bam reads-ref.sorted.bam \
--genome ref.fa \
--scale-events > reads-ref.eventalign.txt

Note

The current version developed by Huxelerate, is able to deliver massive performance on high data volumes, reducing execution times from days to hours using the eventalign tool and compared to software-only executions.