ont-assembly-snake
master @ f4d6add

Workflow Type: Snakemake
Stable

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
Rasusa
Flye
raven
miniasm
Unicycler
Canu
racon
medaka
pilon
Polypolish
POLCA
Homopolish
proovframe

Version History

master @ f4d6add (earliest) Created 6th Mar 2024 at 10:25 by Peter Menzel

run canu as shadow rule to reduce disk space usage

and add comment about Medaka's default model to README


Frozen master f4d6add
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Citation
Menzel, P. (2024). ont-assembly-snake. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.787.1
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Views: 897   Downloads: 294

Created: 6th Mar 2024 at 10:25

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