Query a metaplasmidome database to identify and annotate plasmids in metagenomes 1.0
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Download RO-CrateThis workflow query metagenomic raw data against a metaplasmidome database to identify plasmids and annotate them with genes, KO, PFAM
Associated Tutorial
This workflows is part of the tutorial Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Bérénice Batut, Nadia Goué
Tutorial Author(s): Bérénice Batut, Nadia Goué, Didier Debroas
Tutorial Contributor(s): Björn Grüning, Bérénice Batut
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| KEGG Ortogolog | #main/KEGG Ortogolog | Tabular file with non-redundant KEGG Orthologs and CDS IDs |
|
| Metaplasmidome predicted CDS | #main/Metaplasmidome predicted CDS | GFF file with predicted CDS |
|
| Metaplasmidome sequences | #main/Metaplasmidome sequences | FASTA sequences of the metaplasmidome database |
|
| PFAM | #main/PFAM | Tabular file with non-redundant PFAM and CDS IDs |
|
| Raw metagenomics data | #main/Raw metagenomics data | FASTA files of the raw metagenomics data |
|
Steps
| ID | Name | Description |
|---|---|---|
| 5 | Map with minimap2 | toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0 |
| 6 | Convert FASTA to Tabular | CONVERTER_fasta_to_tabular |
| 7 | Count GFF Features | toolshed.g2.bx.psu.edu/repos/devteam/count_gff_features/count_gff_features/0.2 |
| 8 | Cut | Cut1 |
| 9 | Cut | Cut1 |
| 10 | Compute | toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1 |
| 11 | Histogram with ggplot2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/3.4.0+galaxy0 |
| 12 | Cut | Cut1 |
| 13 | Histogram | toolshed.g2.bx.psu.edu/repos/devteam/histogram/histogram_rpy/1.0.4 |
| 14 | Filter | Filter1 |
| 15 | Histogram with ggplot2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/3.4.0+galaxy0 |
| 16 | Filter | Filter1 |
| 17 | Cut | Cut1 |
| 18 | Cut | Cut1 |
| 19 | Histogram with ggplot2 | toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_histogram/ggplot2_histogram/3.4.0+galaxy0 |
| 20 | Join two Datasets | join1 |
| 21 | Cut | Cut1 |
| 22 | Cut | Cut1 |
| 23 | Add Header | toolshed.g2.bx.psu.edu/repos/estrain/add_column_headers/add_column_headers/0.1.3 |
| 24 | Sort | sort1 |
| 25 | Join two Datasets | join1 |
| 26 | Unique | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/9.3+galaxy1 |
| 27 | Cut | Cut1 |
| 28 | Tabular-to-FASTA | toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1 |
| 29 | Group | Grouping1 |
| 30 | Filter | Filter1 |
| 31 | Cut | Cut1 |
| 32 | Filter by keywords and/or numerical value | toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2021.04.19.1 |
| 33 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 34 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
| 35 | Add Header | toolshed.g2.bx.psu.edu/repos/estrain/add_column_headers/add_column_headers/0.1.3 |
| 36 | Concatenate datasets | cat1 |
| 37 | Join two Datasets | join1 |
| 38 | Cut | Cut1 |
| 39 | Join two Datasets | join1 |
| 40 | Cut | Cut1 |
| 41 | Select last | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1 |
| 42 | Add Header | toolshed.g2.bx.psu.edu/repos/estrain/add_column_headers/add_column_headers/0.1.3 |
| 43 | Filter | Filter1 |
| 44 | Filter | Filter1 |
| 45 | Group | Grouping1 |
| 46 | Group | Grouping1 |
| 47 | Group | Grouping1 |
| 48 | Select last | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1 |
| 49 | Sort | sort1 |
| 50 | Sort | sort1 |
| 51 | Add Header | toolshed.g2.bx.psu.edu/repos/estrain/add_column_headers/add_column_headers/0.1.3 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| CDS annotation overview per metagenomic sequences | #main/CDS annotation overview per metagenomic sequences | n/a |
|
| CDS in metagenomes identified as plasmids | #main/CDS in metagenomes identified as plasmids | n/a |
|
| CDS in metagenomes identified as plasmids + KO + PFAM | #main/CDS in metagenomes identified as plasmids + KO + PFAM | n/a |
|
| Metagenome sequences identified as plasmids | #main/Metagenome sequences identified as plasmids | n/a |
|
| Metagenomes identified as plasmids | #main/Metagenomes identified as plasmids | n/a |
|
Version History
1.0 (earliest) Created 13th Jan 2025 at 13:09 by Helena Rasche
Added/updated 4 files
Open
master13bf4ab
Creators and Submitter
Views: 20 Downloads: 4
Created: 13th Jan 2025 at 13:08
AttributionsNone
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