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	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

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

1.0 (latest)

2.0 (earliest)

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

2.0 (earliest) Created 25th Jun 2024 at 10:58 by Helena Rasche

Creators

Submitter

Building an amplicon sequence variant (ASV) table from 16S data using DADA2 2.0 (earliest) 1.0 (latest) 2.0 (earliest)

Associated Tutorial

Features

Thanks to...

Inputs

Steps

Outputs

Version History

1.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

2.0 (earliest) Created 25th Jun 2024 at 10:58 by Helena Rasche

Creators

Submitter

Related items

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

1.0 (latest)

2.0 (earliest)