Abstract Swine dysentery (SD) caused by Brachyspira hyodysenteriae results in economic losses in swine producing countries GitHub's Skill-Based Volunteering Project Team and Ersilia, an AI non-profit, built an Actions solution that sped up machine Is Microbiology the NEW Gold Standard for Lab-based Research Projects?
ABPHM Lightning Talk - Using Bactopia to process 67,000 Staphylococcus aureus genomes with AWS Batch Bactopia is a flexible, Nextflow based, set of workflows for analysis of bacterial genomes. The default workflow is based on de-novo assembly.
Computational analysis pipelines are a key element of modern science but can be difficult to maintain or export to other systems, 6 girls sing Justin Bieber's "Baby" An overview of Bactopia for the Bioinformatics Showcase at the 2025 APHBM conference.
Day 4 - session 1 Talk: Introduction to DSL2 - Paolo di Tommaso | Seqera Labs. Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools. 2025 Bactopia for genomic epidemiology investigations
How nf-core configs work (nf-core/bytesize #2) This is an unedited video of a 1a audit on the Shelton Police Department in Shelton Washington.
Introduction - Bioinformatics for Genomic Epidemiology March 2024 This is a brief 1 minute overview of Bactopia for the Bioinformatics Showcase at the 2023 APHBM conference.
A brief 1 minute lightning talk giving an overview of my poster on Bactopia, a pipeline for the complete analysis of bacterial Bactopia v3 - enhancements for public health genomic surveillance. Robert Petit, Senior Bioinformatics Scientist at Wyoming
My 2021 Waite Research Institute Showcase video entry talking about my PhD research. Videos were required to be aimed at a k-mer analysis with python: estimating the genome size from raw data [01] bactopia/bactopia: A flexible pipeline for complete analysis - GitHub
The code is The written tutorial is nf-core/bytesize: bactopia & using nf-core components in non-nf-core pipelines Bacterial Analysis
Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. mSystems. 5 (2020). Creators. Petit III, Robert A. ORCID icon · Read, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR221/005/SRR22175105/SRR22175105_1.fastq.gz
Bactopia 2.1.0 - CQLS Software Update List Epigenomics of Common Diseases: Methylation Risk Scores in childhood aeroallergen sensitization
WMConf Lightning Talks - Official trailer (new series) A cannabis pan-genome Bactopia Lightning Talk - Wellcome AMR - Genomes, Big Data and Emerging Technologies conference
This week, Maxime Garcia (@MaxUlysse) will present: How nf-core configs work. This talk will cover: * Making your own Nextflow Ragout - A reference-assisted assembly tool for bacterial genomes - Mikhail Kolmogorov - ISMB 2014
Nextflow v25 Broke Bactopia, So We Rewrote It Robert A Petit III - Senior Bioinformatics Scientist, Wyoming Public Health Nextflow Summit 2022 - Robert Petit Bactopia Overview - ABPHM 2025 Bioinformatics Showcase
We've invited Robert Petit and Tim Read from Emory University to present on Bactopia, "an extensive workflow for processing This is a very brief Lightning Talk for a poster I'll presenting at ABPHM 2021. I this poster titled "Using Bactopia to process 67000
This lightning talk introduces our poster on methylation risk scores in aeroallergen sensitization, which was presented on the If Bacteria were visible naked eye.
Recording of the second webinar of the 2022 SASSB Webinar Series 5 May 2022 Theme: Bacterial genomic diversity Invited Introduction to Nextflow DLS2 with de novo assembly tutorial [keynote] Informatic Methods & Strategies: Parasite Genomes & Genomic Dark Matter by Mr Yuanting
Solenne Correard introduces the nextflow pipeline variantcatalogue. Though not an nf-core pipeline (yet), variantcatalogue is Genomics-guided discovery of fungicidal bacteria - Matthew Biggs - MLCSB - ISMB 2020 Posters.
It is now relatively easy to obtain a high-quality draft genome sequence of a bacterium, but bioinformatic analysis requires organization and optimization Macee, Lexy, Phoebe, Modesta, Destiny and Kenzie singing Justin Bieber's "Baby". All the parents of these girls have given their
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons | RTCL.TV CAB-KUIAS Internationall Series 2022 "Banana genomics and its application:Breeding and world current disease" Friday, In this video I provide a short overview of my poster presented at the SFA2F conference. This poster gives a preview for what you
On April 28th, 2022, I was invited to give a talk about Bactopia to the African Bioinformatics Network. In this talk, I provide a Is It Worth Building a Custom WGS Analysis Pipeline When Bactopia
This tutorial shows you how to analyze whole genome sequence of a bacterial genome. A bioinformatics tutorial on Bacterial Dan was selected to speak at Selenium Conference 2012 in London about an entirely different topic. As part of his presentation, In this webinar, Dan Browne and PacBio Bioinformatics Field Application Scientist, presents on microbial assembly as our latest
Lightning Talks presented by Dan Cuellar #AppiumConf2021 "Explore this detailed guide for microbiology and bioinformatics students, covering essential research methodologies for Rob Lalonde of Seqera Labs interviews Robert Petit, a senior bioinformatics scientist at Wyoming Public Health Laboratory. In this
Nextflow Summit Boston 2023 - Robert Petit Given that Bactopia is well-documented and actively maintained, would it still make sense to build my own pipeline from scratch? Or should I
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. Robert A. Petit III is giving an introduction to bactopia, a nextflow pipeline that is not part of nf-core but is using some of the nf-core Ragout - A reference-assisted assembly tool for bacterial genomes - Mikhail Kolmogorov - ISMB 2014.
Presented: Thursday 4 August 2022 Presenter: Mr Yuanting Zheng Host: Prof. Robin Gasser VetSurgeon DVM PhD DVS nf-core/bytesize: variantcatalogue
Hello everyone! Here is a short talk titled "Integrating Staphopia into Staphylococcus aureus genomic investigations". In this talk I Whole Genome Sequence Analysis | Bacterial Genome Analysis | Bioinformatics 101 for Beginners
DAY 2, MARCH 4 | SESSION VII 00:00 - Lightning Talks: Sustainable Growth Moderated by Maria Vagliasindi, Lead Economist, Bactopia is a flexible pipeline for complete analysis of bacterial genomes. Information Last Updated. at 08:29. License. MIT. Total Downloads.
Roary pan genome tutorial | Bioinformatics tutorial on Pangenome analysis of bacterial genomes [Nextflow DSL2] Running a remote pipeline using Docker Bactopia is an open source system that can scale from projects as small as one bacterial genome to ones including thousands of genomes.
Day 9: morning session working on Bactopia coding with Peter part 2 Episode 7: Pathogens, Bactopia and awesome shirts
20230324 Webinar: Go with the Workflow: NextflowDSL2 Basics Video recorded during the virtual Bioinfoskills for Microbial Genomics workshop - 02 Feb 2022. A talk by Jonathan Eisen given at a conference on "Genomes, Medicine and the Environment" in October 2007. The talk was
Keywords ### #ImageGenerator #desktopapplication #easilygenerate #generatecomparative #comparativegenomic Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial StaPH-B Monthly Webinar - May 2020
This episode of Basic Bioinformatics is a high level review of a bioinformatics pipeline for microbial DNA variants. We will assume Basic Bioinformatics: Overview of a Microbial DNA Variants Pipeline
Unedited 1a audit Shelton PD 👍🏻 08 Working with Nextflow DSL2 modules and Bactopia | Robert Petit
This study evaluates four genomic analysis pipelines—Bactopia, Nullarbor, TORMES, and Nf-core/mag—for detecting antibiotic resistance genes ( Using Bactopia for the complete analysis of bacterial genomes
APRÈS BACC: épisode 11 #Infra4Dev Conference 2022 | DAY 2 | Lightning Talks & Featured Paper Presentations Designing mechanisms into Bactopia to support its users and contribute back to the community. Robert Petit, Senior
How GitHub and Ersilia open sourced endemic disease research in low-and-middle-income countries Bactopia: Introduction With our physical Webmaster Conference events on hold, we are excited to bring you a new series featuring conference-style
Macee Video A step-by-step process of performing pangenome analysis using the tools Prokka and Roary. On bacteria genomes *Thank me Day 9: morning session working on Bactopia with Peter
Bactopia Overview - ABPHM Bioinformatics Showcase Introduction to DSL2 - Paolo Di Tommaso (Day 4_1)
bactopia This is a video of pictures done by my 7 year old using Windows Paint program. Music by Pink - So What.
A demo of how we can share pipelines using: • GitHub to host the code and the configuration • Docker (or Singularity, or even Robert A Petit III: Nextflow v25 Broke Bactopia, So We Rewrote It Introduction to Cholera Case Study - Hands On Lorem Ipsum is simply dummy text of the printing and typesetting industry.
Item - Optimizing ARG Detection in Lysimeter System: A The JBrowse Genome Browser allows the user to view objects such as genes, variants, QTLs, and so forth in their genomic Production : TCHANA Valdo #cinema #africa #humour #music #happy.
A genomic encyclopedia of bacteria and archaea (GEBA) JBrowse Genome Browser Video Tutorial
Comparative Genomics of Tick-Transmitted Bacteria Bioinformatics Lunch & Learn: Better Assemblies of Bacterial Genomes with Microbial Analysis
Towards the Pangenome of banana Genomics-guided discovery of fungicidal bacteria - Matthew Biggs - MLCSB - ISMB 2020 Posters Nick Vereecke: Emergence of new multi-resistant bacteria strains revealed by high-quality WGS
Integrating Staphopia into your Staphylococcus aureus genomic investigations Bacterial genomic diversity: Prof. Luis-Miguel Rodriguez-R, Catherine Brink and Diego Castillo SFA2F Poster - Bactopia v2: Highly scalable, portable and customizable bacterial genome analyses