Workflow Type: Galaxy
Frozen
dada2 amplicon analysis for paired end data
The workflow has three main outputs:
- the sequence table (output of makeSequenceTable)
- the taxonomy (output of assignTaxonomy)
- the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)
Inputs
ID | Name | Description | Type |
---|---|---|---|
Cached reference database | Cached reference database | for taxonomic assignment. If a cached reference is used no reference from history is used. |
|
Paired input data | Paired input data | Paired input data |
|
Pool samples | Pool samples | Pooling may increase sensitivity |
|
Read length forward read | Read length forward read | Forward reads will be truncated to this length. Empty means no truncation. |
|
Read length reverse read | Read length reverse read | Reverse reads will be truncated to this length. Empty means no truncation. |
|
Steps
ID | Name | Description |
---|---|---|
5 | Sort samples | __APPLY_RULES__ |
6 | QualityProfile before filterAndTrim | toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0 |
7 | dada2: filterAndTrim | toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.30.0+galaxy0 |
8 | QualityProfile after filterAndTrim | toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.30.0+galaxy0 |
9 | Unzip collection | __UNZIP_COLLECTION__ |
10 | dada2: learnErrors | toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0 |
11 | dada2: learnErrors | toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.30.0+galaxy0 |
12 | dada2: dada | toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0 |
13 | dada2: dada | toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.30.0+galaxy0 |
14 | dada2: mergePairs | toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.30.0+galaxy0 |
15 | dada2: makeSequenceTable | toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.30.0+galaxy0 |
16 | dada2: removeBimeraDenovo | toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.30.0+galaxy0 |
17 | dada2: sequence counts | toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.30.0+galaxy0 |
18 | dada2: assignTaxonomy | toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.30.0+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Sequence Table | Sequence Table | n/a |
|
Counts | Counts | n/a |
|
Taxonomy | Taxonomy | n/a |
|
Version History
v0.1 (earliest) Created 12th Mar 2024 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
c8f7f99
Creators and Submitter
Creator
Additional credit
UFZ Leipzig
Submitter
License
Activity
Views: 2195 Downloads: 482 Runs: 6
Created: 12th Mar 2024 at 03:01
Tags
Attributions
None