Training: 16S rRNA Sequencing With Mothur: Main Tutorial
1.0

Workflow Type: Galaxy

16S Microbial Analysis with mothur (extended)

Associated Tutorial

This workflows is part of the tutorial Training: 16S rRNA Sequencing With Mothur: Main Tutorial, available in the GTN

Thanks to...

Tutorial Author(s): Saskia Hiltemann, Bérénice Batut, Dave Clements

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
HMP_MOCK.v35.fasta HMP_MOCK.v35.fasta n/a
  • File
Input FASTQ pairs Input FASTQ pairs n/a
  • File[]
mouse.dpw.metadata mouse.dpw.metadata n/a
  • File
silva.v4.fasta silva.v4.fasta n/a
  • File
trainset9_032012.pds.fasta trainset9_032012.pds.fasta n/a
  • File
trainset9_032012.pds.tax trainset9_032012.pds.tax n/a
  • File

Steps

ID Name Description
10 Count.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0
11 Align.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_seqs/mothur_align_seqs/1.39.5.0
12 Summary.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0
13 Screen.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0
14 Filter.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0
15 Unique.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0
16 Pre.cluster toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0
17 Chimera.vsearch toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1
18 Remove.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0
19 Classify.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0
20 Remove.lineage toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0
21 Get.groups toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_groups/mothur_get_groups/1.39.5.0
22 Remove.groups toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0
23 Seq.error toolshed.g2.bx.psu.edu/repos/iuc/mothur_seq_error/mothur_seq_error/1.39.5.0
24 Dist.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0
25 Cluster.split toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0
26 Cluster toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0
27 Make.shared toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0
28 Classify.otu toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0
29 Make.shared toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0
30 Summary.single toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0
31 Count.groups toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0
32 Dist.shared toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0
33 Rarefaction.single toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0
34 Sub.sample toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0
35 Taxonomy-to-Krona toolshed.g2.bx.psu.edu/repos/iuc/mothur_taxonomy_to_krona/mothur_taxonomy_to_krona/1.0
36 Rarefaction.single toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0
37 Tree.shared toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0
38 Heatmap.sim toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0
39 Plotting tool toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2
40 Venn toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0
41 Make.biom toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_biom/mothur_make_biom/1.39.5.0
42 Krona pie chart toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1.1
43 Newick Display toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6
6 Make.contigs toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_contigs/mothur_make_contigs/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 Screen.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0
9 Unique.seqs toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0

Version History

1.0 (earliest) Created 25th Jun 2024 at 10:57 by Helena Rasche

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Created: 25th Jun 2024 at 10:57

Last updated: 25th Jun 2024 at 10:57

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