0: View complete virus identification Version 1
Download RO Crate
Run on usegalaxy.euNon-functional workflow to get a global view of possibilities for plant virus classification.
Steps
| ID | Name | Description |
|---|---|---|
| 0 | fastp | toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 |
| 1 | FLASH merge read | toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.4 |
| 2 | Kraken2 | toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.1.1+galaxy0 |
| 3 | FASTA Merge Files and Filter Unique Sequences | toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 |
| 4 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 |
| 5 | NCBI BLAST+ blastn | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0 |
| 6 | NCBI BLAST+ tblastx | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/2.10.1+galaxy0 |
| 7 | hmmscan | toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.3+galaxy1 |
| 8 | Shovill | toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0 |
| 9 | Convert Kraken | toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.2 |
| 10 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 |
| 11 | Krona pie chart | toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0 |
| 12 | BAM filter: keep unmapped reads | toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 |
| 13 | BAMfilter : keep mapped reads | toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 |
| 14 | SamToFastq | toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2 |
| 15 | Shovill | toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0 |
| 16 | NCBI BLAST+ blastn | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0 |
Version History
Version 1 (earliest) Created 4th Feb 2021 at 09:05 by johan Rollin
Added/updated 1 files
Open
master531b52e
Creators and SubmitterViews: 1250 Downloads: 36
Created: 4th Feb 2021 at 09:05
AttributionsNone
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Teams: Integrated and Urban Plant Pathology Laboratory
Organizations: Liege university
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, Galaxycompchem, 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
Web page: Not specified
Les recherches et enseignements développés par le Laboratoire de Phytopathologie Intégrée et Urbaine visent à améliorer la protection des plantes contre les maladies provoquées par les agents pathogènes et à développer de nouveaux modes de production agricole en milieu urbain. Le laboratoire contribue ainsi à répondre aux défis écologiques, environnementaux, climatiques et sociétaux de l’agriculture de demain.
Space: Independent Teams
Public web page: https://www.gembloux.ulg.ac.be/phytopathologie/
