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pmenzel committed Apr 5, 2024
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# ont-assembly-snake

A Snakemake wrapper for easily creating *de novo* bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data,
A Snakemake wrapper for easily creating *de novo* bacterial isolate genome assemblies from Oxford Nanopore (ONT) sequencing data, and optionally Illumina data,
using any combination of read filtering, assembly, long and short read polishing, and reference-based polishing.

See the preprint here: [Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation, Preprints.org 2022](https://www.preprints.org/manuscript/202208.0191/v1)
The workflow is published in [Snakemake workflows for long-read bacterial genome assembly and evaluation](https://gigabytejournal.com/articles/116) in _GigaByte_.

## Included programs

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