dada2/main

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/1.38.0+galaxy1
7	dada2: filterAndTrim	toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.38.0+galaxy1
8	QualityProfile after filterAndTrim	toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.38.0+galaxy1
9	Unzip collection	__UNZIP_COLLECTION__
10	dada2: learnErrors	toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.38.0+galaxy1
11	dada2: learnErrors	toolshed.g2.bx.psu.edu/repos/iuc/dada2_learnerrors/dada2_learnErrors/1.38.0+galaxy1
12	dada2: dada	toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.38.0+galaxy1
13	dada2: dada	toolshed.g2.bx.psu.edu/repos/iuc/dada2_dada/dada2_dada/1.38.0+galaxy1
14	dada2: mergePairs	toolshed.g2.bx.psu.edu/repos/iuc/dada2_mergepairs/dada2_mergePairs/1.38.0+galaxy1
15	dada2: makeSequenceTable	toolshed.g2.bx.psu.edu/repos/iuc/dada2_makesequencetable/dada2_makeSequenceTable/1.38.0+galaxy1
16	dada2: removeBimeraDenovo	toolshed.g2.bx.psu.edu/repos/iuc/dada2_removebimeradenovo/dada2_removeBimeraDenovo/1.38.0+galaxy1
17	dada2: sequence counts	toolshed.g2.bx.psu.edu/repos/iuc/dada2_seqcounts/dada2_seqCounts/1.38.0+galaxy1
18	dada2: assignTaxonomy	toolshed.g2.bx.psu.edu/repos/iuc/dada2_assigntaxonomyaddspecies/dada2_assignTaxonomyAddspecies/1.38.0+galaxy1

Outputs

ID	Name	Description	Type
Sequence Table	Sequence Table	n/a	File
Counts	Counts	n/a	File
Taxonomy	Taxonomy	n/a	File

Version History

Updated to v0.4

Frozen v0.4 522ad4b

Updated to v0.3

Frozen v0.3 91902e3

Updated to v0.2

Frozen v0.2 584af87

Updated to v0.1

Frozen v0.1 c8f7f99

dada2/main
v0.4 (latest)

v0.4 (latest)

v0.3

v0.2

v0.1 (earliest)