Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] Version 1
Visit source
Download RO-Crate
Run on GalaxyThe workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html and [https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Cleaned Sequences | #main/Cleaned Sequences | n/a |
|
| Count Table | #main/Count Table | n/a |
|
| Training set FASTA | #main/Training set FASTA | n/a |
|
| Training set Taxonomy | #main/Training set Taxonomy | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Classify.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0 |
| 5 | Remove.lineage | toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
Version History
Version 1 (earliest) Created 9th Nov 2023 at 05:16 by Sarah Williams
Initial commit
Open
master884afcc
Creators and Submitter
Views: 3340 Downloads: 205 Runs: 0
Created: 9th Nov 2023 at 05:16
Tags AttributionsNone
Collections
16S Microbial Analy...
Related items
Teams: Galaxy Training Network
Organizations: Erasmus University Medical Centre
https://orcid.org/0000-0003-3803-468X
Post-doc at ErasmusMC, Galaxy Training Network (GTN) Lead
Teams: QCIF Bioinformatics
Organizations: QCIF
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/
The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.
Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...
Maintainers: Sarah Williams, Ahmed Mehdi, Original galaxy workflow developers: Saskia Hiltemann, Bérénice Batut, Dave Clements
Number of items: 7
Tags: Not specified
