Building an amplicon sequence variant (ASV) table from 16S data using DADA2

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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

Thanks to...

Tutorial Author(s): Bérénice Batut

Tutorial Contributor(s): Matthias Bernt, Clea Siguret

Workflow Author(s): , Bérénice Batut

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1105?version=2

Inputs

ID Name Description Type
Raw reads Raw reads raw_reads
  • File[]
header header header
  • File

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
  • File
sequence_counts sequence_counts n/a
  • File
taxons taxons n/a
  • File
metada_table metada_table n/a
  • File

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 Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
dada2
phyloseq
License
MIT License
Activity

Views: 655   Downloads: 171

Created: 25th Jun 2024 at 10:58

Last updated: 25th Jun 2024 at 10:58

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Total size: 241 KB
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