Workflow 3: CFIA Version 1
Download RO Crate
Run on usegalaxy.euWith this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.
This pipeline is based on the work of the National Food Agency of Canada.
Doi: 10.3389/fmicb.2020.00549
Steps
| ID | Name | Description |
|---|---|---|
| 1 | SeqSero - raw allele | toolshed.g2.bx.psu.edu/repos/ddollee/seqsero2/seqsero2/1.2.1+galaxy0 |
| 2 | SRST2 | toolshed.g2.bx.psu.edu/repos/nml/srst2/srst2/0.3.7 |
| 3 | BBTools: BBduk | toolshed.g2.bx.psu.edu/repos/iuc/bbtools_bbduk/bbtools_bbduk/39.01+galaxy0 |
| 4 | Map with KMA | toolshed.g2.bx.psu.edu/repos/iuc/kma/kma_map/1.2.21+galaxy1 |
| 5 | SeqSero2 - raw k-mer | toolshed.g2.bx.psu.edu/repos/ddollee/seqsero2/seqsero2/1.2.1+galaxy0 |
| 6 | hamronize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1 |
| 7 | BBTools: Tadpole | toolshed.g2.bx.psu.edu/repos/iuc/bbtools_tadpole/bbtools_tadpole/39.01+galaxy0 |
| 8 | SPAdes + pilon | toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1 |
| 9 | SKESA + pilon | toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy1 |
| 10 | SeqSero - assemblies | toolshed.g2.bx.psu.edu/repos/ddollee/seqsero2/seqsero2/1.2.1+galaxy0 |
| 11 | Resistance Gene Identifier (RGI) | toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.2.1 |
| 12 | sistr_cmd | toolshed.g2.bx.psu.edu/repos/nml/sistr_cmd/sistr_cmd/1.1.1+galaxy1 |
| 13 | MOB-Recon | toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/3.0.3+galaxy0 |
| 14 | Resistance Gene Identifier (RGI) | toolshed.g2.bx.psu.edu/repos/card/rgi/rgi/5.2.1 |
| 15 | hamronize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1 |
| 16 | hamronize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_tool/hamronize_tool/1.0.3+galaxy1 |
| 17 | hamronize: summarize | toolshed.g2.bx.psu.edu/repos/iuc/hamronize_summarize/hamronize_summarize/1.0.3+galaxy2 |
Version History
Version 0.1 (earliest) Created 24th Nov 2022 at 13:42 by Dennis Dollée
Update workflow
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Creators and SubmitterViews: 1189
Created: 24th Nov 2022 at 13:42
Last updated: 30th Oct 2023 at 16:50
AttributionsNone
Related items
Organizations: Erasmus University Medical Centre
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, Genomics Coordination Center, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, EuroScienceGateway, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC
Web page: Not specified
Space: Independent Teams
Public web page: https://erasmusmc-bioinformatics.github.io/benchAMRking/
