Workflow Type: Galaxy
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Building an amplicon sequence variant (ASV) table from 16S data using DADA2
Associated Tutorial
This workflows is part of the tutorial Building an amplicon sequence variant (ASV) table from 16S data using DADA2, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Bérénice Batut
Tutorial Contributor(s): Matthias Bernt, Clea Siguret
Workflow Author(s): , Bérénice Batut
Inputs
ID | Name | Description | Type |
---|---|---|---|
Raw reads | Raw reads | raw_reads |
|
header | header | header |
|
Steps
ID | Name | Description |
---|---|---|
2 | Sort collection | __SORTLIST__ |
3 | dada2: filterAndTrim | toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.30.0+galaxy0 |
4 | dada2: plotQualityProfile | toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0 |
5 | Unzip collection | __UNZIP_COLLECTION__ |
6 | dada2: plotQualityProfile | toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0 |
7 | dada2: learnErrors | toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0 |
8 | dada2: learnErrors | toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0 |
9 | dada2: dada | toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0 |
10 | dada2: dada | toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0 |
11 | dada2: mergePairs | toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.30.0+galaxy0 |
12 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
13 | dada2: makeSequenceTable | toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0 |
14 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
15 | dada2: removeBimeraDenovo | toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.30.0+galaxy0 |
16 | Select first | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/9.3+galaxy1 |
17 | dada2: sequence counts | toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0 |
18 | dada2: assignTaxonomy and addSpecies | toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0 |
19 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0 |
20 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
21 | Concatenate datasets | cat1 |
22 | Create phyloseq object | toolshed.g2.bx.psu.edu/repos/iuc/phyloseq_from_dada2/phyloseq_from_dada2/1.46.0+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
sequence_table | sequence_table | n/a |
|
sequence_counts | sequence_counts | n/a |
|
taxons | taxons | n/a |
|
metada_table | metada_table | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche
Added/updated 4 files
Open
master
242aa01
2.0 (earliest) Created 25th Jun 2024 at 10:58 by Helena Rasche
Added/updated 4 files
Frozen
2.0
411b7a5
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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Views: 198 Downloads: 76
Created: 25th Jun 2024 at 10:58
Last updated: 25th Jun 2024 at 10:58
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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