16S_biodiversity_for_overlap_paired_end Version 1
Download RO-Crate
Run on GalaxyMetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| "Input Dataset Collection" | "Input Dataset Collection" | n/a |
|
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 |
|
| _anonymous_output_25 | _anonymous_output_25 | n/a |
|
Version History
Version 1 (earliest) Created 10th Nov 2021 at 00:15 by Mike Thang
Added/updated 1 files
Open
mastera6efa8a
Creators and SubmitterViews: 4530 Downloads: 291 Runs: 0
Created: 10th Nov 2021 at 00:15
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Teams: Galaxy Australia, QCIF Bioinformatics
Organizations: QCIF
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Space: Australian BioCommons
Public web page: https://www.qcif.edu.au/
This ARDC and BioCommons sponsored project delivers a key component of BioCommon’s vision for an ecosystem of platforms providing researchers with sophisticated data analysis and digital asset stewardship capabilities. The Bring Your Own Data (BYOD) Platform (https://www.biocommons.org.au/byod-expansion) has enabled highly accessible, highly available, highly scalable analysis and data sharing capabilities for the benefit of life science researchers nationally.
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