2: Plant virus confirmation Version 1
Download RO-Crate
Run on GalaxyMapping against all plant virus then make contig out of the mapped reads then blast them.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Data_R1.fastq | Data_R1.fastq | n/a |
|
| Data_R2.fastq | Data_R2.fastq | 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 |
| 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 |
|---|---|---|---|
| reference_fasta | reference_fasta | n/a |
|
| Read_mapping_alignement | Read_mapping_alignement | n/a |
|
| mapped_read | mapped_read | n/a |
|
| Paired-end forward | Paired-end forward | n/a |
|
| Paired-end reverse | Paired-end reverse | n/a |
|
| Contigs | Contigs | n/a |
|
| Log file | Log file | n/a |
|
| blastn result | blastn result | 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: 3897 Downloads: 317 Runs: 0
Created: 4th Feb 2021 at 09:10
Last updated: 10th Feb 2023 at 10:06
AttributionsNone
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Teams: Integrated and Urban Plant Pathology Laboratory
Organizations: Liege university
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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.
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Public web page: https://www.gembloux.ulg.ac.be/phytopathologie/
