<![CDATA[BOL: Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes]]> https://bioinformaticsonline.com/bookmarks/view/44539/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes? https://bioinformaticsonline.com/bookmarks/view/44539/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes Wed, 15 May 2024 14:36:12 -0500 https://bioinformaticsonline.com/bookmarks/view/44539/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes <![CDATA[Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes]]> Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactopia Tools.

Bactopia Analysis Pipeline is the main per-isolate workflow in Bactopia. Built with Nextflow, input FASTQs (local or available from SRA/ENA) are put through numerous analyses including: quality control, assembly, annotation, minmer sketch queries, sequence typing, and more.

Bactopia Overview

Bactopia Tools are a set a independent workflows fo

Address of the bookmark: https://github.com/bactopia/bactopia

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