# ont-assembly-snake
A Snakemake wrapper for easily creating *de novo* bacterial 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.
## Included programs
| read filtering | assembly | long read polishing | short read polishing | reference-based polishing |
| --- | --- | --- | --- | --- |
| [Filtlong](https://github.com/rrwick/Filtlong)
[Rasusa](https://github.com/mbhall88/rasusa) | [Flye](https://github.com/fenderglass/Flye)
[raven](https://github.com/lbcb-sci/raven)
[miniasm](https://github.com/lh3/miniasm)
[Unicycler](https://github.com/rrwick/Unicycler)
[Canu](https://github.com/marbl/canu) | [racon](https://github.com/lbcb-sci/racon)
[medaka](https://github.com/nanoporetech/medaka) | [pilon](https://github.com/broadinstitute/pilon/wiki)
[Polypolish](https://github.com/rrwick/Polypolish)
[POLCA](https://github.com/alekseyzimin/masurca#polca) | [Homopolish](https://github.com/ythuang0522/homopolish)
[proovframe](https://github.com/thackl/proovframe) |