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A bacterial pathogen genomics workflow inspired by Nullarbor

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lgi-onehealth/orkas

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orkas: a Nextflow pipeline for bacterial pathogen genomics

Warning This workflow is under active development

Background

Motivation

Pipeline elements

Sequencing reads quality control

Speciation

Assembly

Typing and gene detection

Mask detection

Variant calling

Alignment

Phylogenetic reconstruction

Running orkas

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A bacterial pathogen genomics workflow inspired by Nullarbor

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