Workflow Type: Galaxy

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.
  • string
Paired input data Paired input data Paired input data
  • File[]
Pool samples Pool samples Pooling may increase sensitivity
  • string
Read length forward read Read length forward read Forward reads will be truncated to this length. Empty means no truncation.
  • int?
Read length reverse read Read length reverse read Reverse reads will be truncated to this length. Empty means no truncation.
  • int?

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
  • File
Counts Counts n/a
  • File
Taxonomy Taxonomy n/a
  • File

Version History

v0.2 (latest) Created 30th May 2024 at 11:35 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 584af87

v0.1 (earliest) Created 12th Mar 2024 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 c8f7f99
help Creators and Submitter
Creator
  • Matthias Bernt
Additional credit

UFZ Leipzig

Submitter
License
Activity

Views: 2195   Downloads: 482   Runs: 6

Created: 12th Mar 2024 at 03:01

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