dada2/main

View on GitHub Download RO-Crate Run on Galaxy
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)

SEEK ID: https://workflowhub.eu/workflows/790?version=1

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/1.28+galaxy0
7 dada2: filterAndTrim toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.28+galaxy0
8 QualityProfile after filterAndTrim toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.28+galaxy0
9 Unzip collection __UNZIP_COLLECTION__
10 dada2: learnErrors toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.28+galaxy0
11 dada2: learnErrors toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.28+galaxy0
12 dada2: dada toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.28+galaxy0
13 dada2: dada toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.28+galaxy0
14 dada2: mergePairs toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.28+galaxy0
15 dada2: makeSequenceTable toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.28+galaxy0
16 dada2: removeBimeraDenovo toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.28+galaxy0
17 dada2: sequence counts toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.28+galaxy0
18 dada2: assignTaxonomy toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.28+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
MIT License
Activity

Views: 2084   Downloads: 461   Runs: 0

Created: 12th Mar 2024 at 03:01

help Attributions

None

Total size: 88 KB
Powered by
 (v.1.16.0-main)
About WorkflowHub | Acknowledgements | Credits | Terms & Conditions | Privacy Policy | Cite us | Contact us
Copyright © 2008 - 2024 The University of Manchester and HITS gGmbH