MGnify's amplicon pipeline v5.0 - rRNA prediction
1.0

Workflow Type: Galaxy

Classification and visualization of SSU, LSU sequences.

Associated Tutorial

This workflows is part of the tutorial MGnify v5.0 Amplicon Pipeline, available in the GTN

Features

Thanks to...

Workflow Author(s): EMBL's European Bioinformatics Institute, Rand Zoabi, Paul Zierep

Tutorial Author(s): Rand Zoabi

Funder(s): German Competence Center Cloud Technologies for Data Management and Processing (de.KCD)

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Clan information file Clan information file This file lists which models belong to the same clan.
  • File
Processed sequences Processed sequences Post quality control.
  • File[]

Steps

ID Name Description
2 cmsearch toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.5+galaxy0
3 Filter empty datasets __FILTER_EMPTY_DATASETS__
4 CMsearch deoverlap toolshed.g2.bx.psu.edu/repos/rnateam/cmsearch_deoverlap/cmsearch_deoverlap/0.08+galaxy2
5 Query Tabular toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
6 SSU BED forward toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
7 SSU BED reverse toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
8 LSU BED forward toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
9 LSU BED reverse toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
10 SSU BED toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
11 LSU BED toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
12 Filter empty datasets __FILTER_EMPTY_DATASETS__
13 Filter empty datasets __FILTER_EMPTY_DATASETS__
14 Concatenate toolshed.g2.bx.psu.edu/repos/devteam/concat/gops_concat_1/1.0.1
15 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
16 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
17 Filter collection __FILTER_FROM_FILE__
18 Filter collection __FILTER_FROM_FILE__
19 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0
20 bedtools getfasta toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.31.1+galaxy0
21 FASTA Width toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2
22 FASTA Width toolshed.g2.bx.psu.edu/repos/devteam/fasta_formatter/cshl_fasta_formatter/1.0.1+galaxy2
23 MAPseq toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0
24 MAPseq toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0
25 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
26 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
27 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
28 Filter empty datasets __FILTER_EMPTY_DATASETS__
29 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
30 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
31 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy0
32 Filter empty datasets __FILTER_EMPTY_DATASETS__
33 Filter empty datasets __FILTER_EMPTY_DATASETS__
34 Filter empty datasets __FILTER_EMPTY_DATASETS__
35 Filter empty datasets __FILTER_EMPTY_DATASETS__
36 Map empty/not empty collection to boolean n/a
37 Filter empty datasets __FILTER_EMPTY_DATASETS__
38 Filter empty datasets __FILTER_EMPTY_DATASETS__
39 Filter empty datasets __FILTER_EMPTY_DATASETS__
40 Map empty/not empty collection to boolean n/a
41 Map empty/not empty collection to boolean n/a
42 Krona SSU SILVA toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
43 Map empty/not empty collection to boolean n/a
44 Krona LSU SILVA toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
45 HDF5 SSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
46 JSON SSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
47 HDF5 LSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
48 JSON LSU SILVA toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1

Outputs

ID Name Description Type
LSU and SSU BED regions LSU and SSU BED regions n/a
  • File
SSU FASTA files SSU FASTA files n/a
  • File
LSU FASTA files LSU FASTA files n/a
  • File
SSU taxonomic classifications using SILVA DB SSU taxonomic classifications using SILVA DB n/a
  • File
SSU OTU tables (SILVA DB) SSU OTU tables (SILVA DB) n/a
  • File
LSU taxonomic classifications using SILVA DB LSU taxonomic classifications using SILVA DB n/a
  • File
LSU OTU tables (SILVA DB) LSU OTU tables (SILVA DB) n/a
  • File
SSU taxonomic abundance pie charts (SILVA DB) SSU taxonomic abundance pie charts (SILVA DB) n/a
  • File
LSU taxonomic abundance pie charts (SILVA DB) LSU taxonomic abundance pie charts (SILVA DB) n/a
  • File
SSU OTU tables in HDF5 format (SILVA DB) SSU OTU tables in HDF5 format (SILVA DB) n/a
  • File
SSU OTU tables in JSON format (SILVA DB) SSU OTU tables in JSON format (SILVA DB) n/a
  • File
LSU OTU tables in HDF5 format (SILVA DB) LSU OTU tables in HDF5 format (SILVA DB) n/a
  • File
LSU OTU tables in JSON format (SILVA DB) LSU OTU tables in JSON format (SILVA DB) n/a
  • File

Version History

1.0 (earliest) Created 4th Aug 2025 at 14:16 by GTN Bot

Added/updated 4 files


Open master da5ec70
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Created: 4th Aug 2025 at 14:16

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