Hugenomic Nanopolish

Analyze more than 800,000 long reads of genomic data (~ 102 GB) in 3 hours thanks to Huxelerate Hugenomic Nanopolish(*).

Huxelerate Hugenomic Nanopolish enables ultra-fast signal-level analysis of large datasets of Oxford Nanopore Sequencing data.

This AMI is a CentOS Linux image and comes pre-installed with Hugenomic Nanopolish developed by Huxelerate. The software is based on Nanopolish and can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more.

The accelerated implementation exploits FPGAs to speedup the computation and provide high performance and faster time to result. This release allows to accelerate the eventalign tool, reducing computational time from days to hours when compared to software-only executions on AWS.

The functionalities provided in this AMI, mirror Nanopolish v0.13.2, please refer to the guide provided by the Nanopolish Team (Nanopolish Guide)

Academic License

Huxelerate provides free access to this AMI to academic users for their research. If you are interested, send an email to Huxelerate at


For any issue in using the instance, please email the Huxelerate Developers Team (


(*) dataset: ; flowcell_id: FAB42451; reads: 818,420; bases: 5,228,838,859; mean: 6389; n50: 10,490; Software equivalent tested on C4.8xlarge using 36 cores took 17,25 hours.