16S_biodiversity_for_overlap_paired_end
Version 1

Workflow Type: Galaxy
Stable

MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

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 Pear toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1
4 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
5 Concatenate datasets cat1
6 Map with BWA-MEM toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
7 MergeSamFiles toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MergeSamFiles/2.18.2.1
8 FilterSamReads toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_FilterSamReads/2.18.2.1
9 Samtools fastx toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
10 VSearch search toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/2.8.3.1
11 VSearch dereplication toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/2.8.3.0
12 VSearch chimera detection toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_chimera_detection/2.8.3.0
13 VSearch clustering toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_clustering/2.8.3.0
14 VSearch search toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_search/2.8.3.1
15 Add column addValue
16 Cut Cut1
17 Cut Cut1
18 Concatenate datasets cat1
19 OTUTable toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_uc2otutable/uclust2otutable/1.0.0
20 Convert toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.5.3
21 BIOM metadata toolshed.g2.bx.psu.edu/repos/iuc/biom_add_metadata/biom_add_metadata/2.1.5.0
22 Phyloseq DESeq2 toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_deseq2/phyloseq_DESeq2/1.22.3
23 Phyloseq Richness toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_richness/phyloseq_richness/1.22.3.2
24 Phyloseq Abundance plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_factor/phyloseq_abundance/1.22.3.3
25 Phyloseq Abundance Taxonomy toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_abundance_taxonomy/phyloseq_taxonomy/1.22.3.3
26 Symmetric Plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_symmetric_plot/symmetricPlot/1.0.1
27 Phyloseq Network Plot toolshed.g2.bx.psu.edu/repos/qfabrepo/metadegalaxy_phyloseq_net/phyloseq_net/1.24.2

Outputs

ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
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_anonymous_output_2 _anonymous_output_2 n/a
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_anonymous_output_3 _anonymous_output_3 n/a
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_anonymous_output_4 _anonymous_output_4 n/a
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_anonymous_output_5 _anonymous_output_5 n/a
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_anonymous_output_6 _anonymous_output_6 n/a
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_anonymous_output_7 _anonymous_output_7 n/a
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_anonymous_output_8 _anonymous_output_8 n/a
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_anonymous_output_9 _anonymous_output_9 n/a
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_anonymous_output_10 _anonymous_output_10 n/a
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_anonymous_output_11 _anonymous_output_11 n/a
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_anonymous_output_12 _anonymous_output_12 n/a
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_anonymous_output_13 _anonymous_output_13 n/a
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_anonymous_output_14 _anonymous_output_14 n/a
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_anonymous_output_15 _anonymous_output_15 n/a
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_anonymous_output_16 _anonymous_output_16 n/a
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_anonymous_output_17 _anonymous_output_17 n/a
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_anonymous_output_18 _anonymous_output_18 n/a
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_anonymous_output_19 _anonymous_output_19 n/a
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_anonymous_output_20 _anonymous_output_20 n/a
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_anonymous_output_21 _anonymous_output_21 n/a
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_anonymous_output_22 _anonymous_output_22 n/a
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_anonymous_output_23 _anonymous_output_23 n/a
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_anonymous_output_24 _anonymous_output_24 n/a
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_anonymous_output_25 _anonymous_output_25 n/a
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Version History

Version 1 (earliest) Created 10th Nov 2021 at 00:15 by Mike Thang

Added/updated 1 files


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Views: 4341   Downloads: 265   Runs: 0

Created: 10th Nov 2021 at 00:15

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