2: Plant virus confirmation Version 1
Download RO Crate
Run on usegalaxy.euMapping against all plant virus then make contig out of the mapped reads then blast them.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| batchmode | batchmode | runtime parameter for tool FASTA Merge Files and Filter Unique Sequences | n/a |
| Data_R1.fastq | Data_R1.fastq | n/a | n/a |
| Data_R2.fastq | Data_R2.fastq | n/a | n/a |
| fastq_input | fastq_input | runtime parameter for tool Map with minimap2 | n/a |
| fastq_input | fastq_input | runtime parameter for tool Map with minimap2 | n/a |
| reference_source | reference_source | runtime parameter for tool Map with minimap2 | n/a |
| excludebed | excludebed | runtime parameter for tool BAM filter | n/a |
| includebed | includebed | runtime parameter for tool BAM filter | n/a |
| infile | infile | runtime parameter for tool BAM filter | n/a |
| input | input | runtime parameter for tool Samtools stats | n/a |
| inputFile | inputFile | runtime parameter for tool SamToFastq | n/a |
| library | library | runtime parameter for tool Shovill | n/a |
| library | library | runtime parameter for tool Shovill | n/a |
| output | output | runtime parameter for tool NCBI BLAST+ blastn | n/a |
| output | output | runtime parameter for tool NCBI BLAST+ blastn | n/a |
| output | output | runtime parameter for tool NCBI BLAST+ blastn | n/a |
| query | query | runtime parameter for tool NCBI BLAST+ blastn | n/a |
Steps
| ID | Name | Description |
|---|---|---|
| 0 | Merge fasta together | Merge several fasta in a multi-fasta file to be use as reference for mapping. WARNING: If two fasta with the same header are provided only one will be kept toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0 |
| 1 | Data_R1.fastq | |
| 2 | Data_R2.fastq | |
| 3 | Map with minimap2 | Map the input reads against the chosen reference fasta file. Multiple mapping The correct placement of a read may be ambiguous, e.g. due to repeats. In this case, there may be multiple read alignments for the same read. One of these alignments is considered primary. All the other alignments have the secondary alignment flag set in the SAM records that represent them. All the SAM records have the same QNAME and the same values for 0x40 and 0x80 flags. Typically the alignment designated primary is the best alignment, but the decision may be arbitrary. toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy2 |
| 4 | BAM filter | Keep only mapped read to perform faster assembly later. toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 |
| 5 | Samtools stats | Obtain stats on the bam file toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 |
| 6 | SamToFastq | Extract read from bam as fastq sequence. Remove secondary alignement reads (that are mapped several time) toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_SamToFastq/2.18.2.2 |
| 7 | Fast assembly (shovill => megahit) | Make contig out of candidate read. toolshed.g2.bx.psu.edu/repos/iuc/shovill/shovill/1.1.0+galaxy0 |
| 8 | BLASTn | Blast contig against precise database to find closest reference toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| output | output | n/a | |
| alignment_output | alignment_output | n/a | |
| outfile | outfile | n/a | |
| output | output | n/a | |
| fq_single | fq_single | n/a | |
| interleaved_fastq | interleaved_fastq | n/a | |
| fq1 | fq1 | n/a | |
| fq2 | fq2 | n/a | |
| fq_u | fq_u | n/a | |
| shovill_std_log | shovill_std_log | n/a | |
| contigs | contigs | n/a | |
| contigs_graph | contigs_graph | n/a | |
| output1 | output1 | n/a |
Version History
Version 1 (earliest) Created 4th Feb 2021 at 09:10 by johan Rollin
Added/updated 1 files
Open
master64469c6
Creators and SubmitterViews: 681 Downloads: 37
Created: 4th Feb 2021 at 09:10
Last used: 26th Jun 2022 at 07:07
AttributionsNone
Related items
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
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/
