Training: 16S rRNA Sequencing With Mothur: Main Tutorial 1.0
Visit source
Download RO-Crate16S 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
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| HMP_MOCK.v35.fasta | HMP_MOCK.v35.fasta | n/a |
|
| Input FASTQ pairs | Input FASTQ pairs | n/a |
|
| mouse.dpw.metadata | mouse.dpw.metadata | n/a |
|
| silva.v4.fasta | silva.v4.fasta | n/a |
|
| trainset9_032012.pds.fasta | trainset9_032012.pds.fasta | n/a |
|
| trainset9_032012.pds.tax | trainset9_032012.pds.tax | n/a |
|
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
Added/updated 4 files
Open
mastere4d3e6e
Creators and Submitter
Views: 430 Downloads: 115
Created: 25th Jun 2024 at 10:57
Last updated: 25th Jun 2024 at 10:57
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
