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 |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
|
| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
| _anonymous_output_10 | _anonymous_output_10 | n/a |
|
| _anonymous_output_11 | _anonymous_output_11 | n/a |
|
| _anonymous_output_12 | _anonymous_output_12 | n/a |
|
| _anonymous_output_13 | _anonymous_output_13 | n/a |
|
| _anonymous_output_14 | _anonymous_output_14 | n/a |
|
| _anonymous_output_15 | _anonymous_output_15 | n/a |
|
| _anonymous_output_16 | _anonymous_output_16 | n/a |
|
| _anonymous_output_17 | _anonymous_output_17 | n/a |
|
| _anonymous_output_18 | _anonymous_output_18 | n/a |
|
| _anonymous_output_19 | _anonymous_output_19 | n/a |
|
| _anonymous_output_20 | _anonymous_output_20 | n/a |
|
| _anonymous_output_21 | _anonymous_output_21 | n/a |
|
| _anonymous_output_22 | _anonymous_output_22 | n/a |
|
| _anonymous_output_23 | _anonymous_output_23 | n/a |
|
| _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: 4318 Downloads: 263 Runs: 0
Created: 10th Nov 2021 at 00:15
Tags AttributionsNone
Collections
BioCommons ‘Bring Y...
Related items
Teams: Galaxy Australia, QCIF Bioinformatics
Organizations: QCIF
https://orcid.org/0000-0002-1480-3563
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
Web page: https://www.biocommons.org.au/
Working closely with researchers, the QCIF Bioinformatics team apply data management, processing, integration, analysis and visualisation techniques to maximise the potential value of biological and clinical data sets. QCIF Bioinformatics is a partner in the Australian BioCommons.
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.
**This WorkflowHub collection ...
