Workflow Type: Galaxy
Open
Work-in-progress
Non-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
master
531b52e
Creators and Submitter
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License
Activity
Views: 3679 Downloads: 286 Runs: 0
Created: 4th Feb 2021 at 09:05
Attributions
None