16S Microbial Analysis with mother - howto Version 1
This document is adapted from 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]. Please also go through these tutorials for better understandings. Note: The steps mentioned in this document are well suited for V3-V4 regions. However the parameters could be varied if your data is related to other regions.
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16S_workflow_documentation.pdf
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Created: 9th Nov 2023 at 05:30
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Version 1 (earliest) Created 9th Nov 2023 at 05:30 by Sarah Williams
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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
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