Workflow Type: Galaxy
Open
Stable
Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "Metabarcoding/eDNA through Obitools" .
This workflow allows to analyze DNA metabarcoding / eDNA data produced on Illumina sequencers using the OBITools.
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
Version 1 (earliest) Created 9th Nov 2023 at 12:41 by Yvan Le Bras
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Views: 2975 Downloads: 198 Runs: 0
Created: 9th Nov 2023 at 12:41
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