16S_biodiversity_for_nonoverlap_paired_end
Version 1

Download RO Crate

Run on usegalaxy.eu

Workflow Type: Galaxy

Stable

No description specified

SEEK ID: https://workflowhub.eu/workflows/233?version=1

Inputs

ID	Name	Description	Type
"Input Dataset Collection"	"Input Dataset Collection"	n/a	File[]

Steps

ID	Name	Description
1	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
2	Trimmomatic	toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.6
3	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.0
4	FastQC	toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
5	Map with BWA-MEM	toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
6	FilterSamReads	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1
7	Samtools fastx	toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
8	VSearch search	toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/2.8.3.1
9	VSearch dereplication	toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0
10	VSearch chimera detection	toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_chimera_detection/1.9.7.0
11	VSearch clustering	toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/1.9.7.0
12	VSearch search	toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/2.8.3.1
13	Add column	addValue
14	Cut	Cut1
15	Cut	Cut1
16	Concatenate datasets	cat1
17	OTUTable	toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_uc2otutable/uclust2otutable/1.0.0
18	Convert BIOM	toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.5.0
19	BIOM metadata	toolshed.g2.bx.psu.edu/repos/iuc/biom_add_metadata/biom_add_metadata/2.1.5.0
20	Phyloseq DESeq2	toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_deseq2/phyloseq_DESeq2/1.22.3
21	Phyloseq Richness	toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_richness/phyloseq_richness/1.22.3.2
22	Phyloseq Abundance plot	toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_factor/phyloseq_abundance/1.22.3.3
23	Phyloseq Abundance Taxonomy	toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_taxonomy/phyloseq_taxonomy/1.22.3.3
24	Phyloseq Network Plot	toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_net/phyloseq_net/1.24.2
25	Symmetric Plot	toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_symmetric_plot/symmetricPlot/1.0.1

Outputs

ID	Name	Description	Type
_anonymous_output_1	_anonymous_output_1	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File
_anonymous_output_8	_anonymous_output_8	n/a	File
_anonymous_output_9	_anonymous_output_9	n/a	File
_anonymous_output_10	_anonymous_output_10	n/a	File
_anonymous_output_11	_anonymous_output_11	n/a	File
_anonymous_output_12	_anonymous_output_12	n/a	File
_anonymous_output_13	_anonymous_output_13	n/a	File
_anonymous_output_14	_anonymous_output_14	n/a	File