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  3. Hugenomic Nanopolish

Hugenomic Nanopolish

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Hugenomic Nanopolish

Huxelerate Hugenomic Nanopolish offers all the benefts of Nanopolish eventalign module with 10 times performance improvement. Huxelerate Hugenomic Nanopolish is able to analyze more than 800,000 long reads of genomic data (about 102 GB) in 3 hours. Thanks to an accelerated FPGA implementation, it provides higher performance and faster time to result, while keeping the same precision of the original tool.

Vendor: Huxelerate

Last Update: February 22, 2021

Size: 320.05 MB

Container Version: v1.0

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This Product is free to deploy from Xilinx.

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Deployment Options

This application is containerized and can be easily run in a few minutes in the cloud, or on-premises.

Cloud Services
AWS
  • Xilinx Runtime: 2019.2
  • Instance Type: f1.2xlarge
  • AMI: FPGA Developer AMI (version 1.8.1)

Getting Started

Follow the instructions based on your deployment method.

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AWS

1.

Install and configue docker 

    git clone https://github.com/Xilinx/Xilinx_Base_Runtime.git

sudo Xilinx_Base_Runtime/utilities/docker_install.sh

2.

Application Execution

Upload cred.json file (get from step 1) to AWS instance in folder /opt/xilinx/cred.json. Then chmod 777 cred.json.

Execute following commands:

    source Xilinx_Base_Runtime/utilities/xilinx_aws_docker_setup.sh

# download example dataset: on this example we already run minimap2 
# and samtools to prepare the dataset and generated a golden dataset
# sorted for comparison

wget https://huxelerate-public.s3.amazonaws.com/ecoli-nanopolish-accelize-example/ecoli_2kb_region_nanopolish_example.tar

# untar example dataset
tar xzf  ecoli_2kb_region_nanopolish_example.tar

# index the reads
sudo docker run $XILINX_AWS_DOCKER_DEVICES -v /opt/xilinx/cred.json:/usr/share/hugenomic/cred.json -v $PWD/ecoli_2kb_region_nanopolish_example:/ecoli_2kb_region_nanopolish_example hubxilinx/huxelerate_nanopolish_aws_f1 index -d /ecoli_2kb_region_nanopolish_example/fast5_files/ /ecoli_2kb_region_nanopolish_example/reads.fasta

# align the nanopore events to the reference genome
sudo docker run $XILINX_AWS_DOCKER_DEVICES -v /opt/xilinx/cred.json:/usr/share/hugenomic/cred.json -v $PWD/ecoli_2kb_region_nanopolish_example:/ecoli_2kb_region_nanopolish_example hubxilinx/huxelerate_nanopolish_aws_f1 eventalign --reads /ecoli_2kb_region_nanopolish_example/reads.fasta --bam /ecoli_2kb_region_nanopolish_example/reads-ref.sorted.bam --genome /ecoli_2kb_region_nanopolish_example/ref.fa --scale-events > ./ecoli_2kb_region_nanopolish_example/reads-ref.eventalign.txt


Checkout Huxelerate user guide.

3.

Results

    # assess the eventalign output
head ./ecoli_2kb_region_nanopolish_example/reads-ref.eventalign.txt

# sort the output for comparison
sort ./ecoli_2kb_region_nanopolish_example/reads-ref.eventalign.txt > ./ecoli_2kb_region_nanopolish_example/reads-ref.eventalign.sorted.txt

# compare the results with the golden output
diff ./ecoli_2kb_region_nanopolish_example/reads-ref.eventalign.golden.sorted.txt ./ecoli_2kb_region_nanopolish_example/reads-ref.eventalign.sorted.txt