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 and [https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
Inputs
ID | Name | Description | Type |
---|---|---|---|
Aligned Sequences | #main/Aligned Sequences | n/a |
|
Count Table | #main/Count Table | n/a |
|
Steps
ID | Name | Description |
---|---|---|
2 | Summary.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 |
3 | Screen.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1 |
4 | Filter.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0 |
5 | Unique.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0 |
6 | Pre.cluster | toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0 |
7 | Summary.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 |
8 | Chimera.vsearch | toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1 |
9 | Remove.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.39.5.0 |
10 | Summary.seqs | toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Summary.seqs on input dataset(s): summary | #main/Summary.seqs on input dataset(s): summary | n/a |
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_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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_anonymous_output_10 | #main/_anonymous_output_10 | n/a |
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_anonymous_output_11 | #main/_anonymous_output_11 | n/a |
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_anonymous_output_12 | #main/_anonymous_output_12 | n/a |
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_anonymous_output_13 | #main/_anonymous_output_13 | n/a |
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_anonymous_output_14 | #main/_anonymous_output_14 | n/a |
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_anonymous_output_15 | #main/_anonymous_output_15 | n/a |
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_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
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_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
_anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
_anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
Version 1 (earliest) Created 9th Nov 2023 at 05:11 by Sarah Williams
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Created: 9th Nov 2023 at 05:11
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