Workflow constructed from history 'Tuto Obitools' 1.0
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Run on GalaxyMetabarcoding/eDNA through Obitools
Associated Tutorial
This workflows is part of the tutorial Metabarcoding/eDNA through Obitools, available in the GTN
Thanks to...
Tutorial Author(s): Coline Royaux, Olivier Norvez, Eric Coissac, Frédéric Boyer, Yvan Le Bras
Tutorial Contributor(s): Helena Rasche, Anne Fouilloux, Yvan Le Bras, Cristóbal Gallardo, Saskia Hiltemann
Funder(s): Pôle National de Données de Biodiversité
Grants(s): Gallantries: Bridging Training Communities in Life Science, Environment and Health
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| wolf_tutorial.zip?download=1 | wolf_tutorial.zip?download=1 | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Illuminapairedend | toolshed.g2.bx.psu.edu/repos/iuc/obi_illumina_pairend/obi_illumina_pairend/1.2.13 |
| 2 | Unzip | toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/0.2 |
| 3 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 |
| 4 | FASTQ Groomer | toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5 |
| 5 | obigrep | toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13 |
| 6 | Line/Word/Character count | wc_gnu |
| 7 | Line/Word/Character count | wc_gnu |
| 8 | NGSfilter | toolshed.g2.bx.psu.edu/repos/iuc/obi_ngsfilter/obi_ngsfilter/1.2.13 |
| 9 | obiuniq | toolshed.g2.bx.psu.edu/repos/iuc/obi_uniq/obi_uniq/1.2.13 |
| 10 | obiannotate | toolshed.g2.bx.psu.edu/repos/iuc/obi_annotate/obi_annotate/1.2.13 |
| 11 | obistat | toolshed.g2.bx.psu.edu/repos/iuc/obi_stat/obi_stat/1.2.13 |
| 12 | obigrep | toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13 |
| 13 | obigrep | toolshed.g2.bx.psu.edu/repos/iuc/obi_grep/obi_grep/1.2.13 |
| 14 | obiclean | toolshed.g2.bx.psu.edu/repos/iuc/obi_clean/obi_clean/1.2.13 |
| 15 | NCBI BLAST+ blastn | toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0 |
| 16 | Filter sequences by ID | toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7 |
| 17 | Filter sequences by ID | toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.7 |
| 18 | obitab | toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13 |
| 19 | obitab | toolshed.g2.bx.psu.edu/repos/iuc/obi_tab/obi_tab/1.2.13 |
| 20 | Join two Datasets | join1 |
| 21 | Join two Datasets | join1 |
| 22 | Cut | Cut1 |
| 23 | Filter | Filter1 |
Version History
master
Creators and Submitter
Views: 1146 Downloads: 161 Runs: 0
Created: 2nd Jun 2025 at 11:05
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
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The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
