preparing genomic data for phylogeny recostruction (GTN)
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Download RO-CrateThis workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. The alignments are cleaned with ClipKIT and the concatenation matrix is built using PhyKit. This can be used for phylogeny reconstruction.
Associated Tutorial
This workflows is part of the tutorial preparing genomic data for phylogeny recostruction (GTN), available in the GTN
Thanks to...
Tutorial Author(s): Miguel Roncoroni, Brigida Gallone
Workflow Author(s): Miguel Roncoroni
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input genomes as collection | #main/Input genomes as collection | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
| 2 | RepeatMasker | toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0 |
| 3 | Funannotate predict annotation | toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2 |
| 4 | Extract ORF | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02 |
| 5 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1 |
| 6 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 7 | Proteinortho | toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1 |
| 8 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 |
| 9 | Filter | Filter1 |
| 10 | Proteinortho grab proteins | toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1 |
| 11 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1 |
| 12 | ClustalW | toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1 |
| 13 | ClipKIT. Alignment trimming software for phylogenetics. | toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0 |
| 14 | PhyKit - Alignment-based functions | toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| A partition file ready for input into RAxML or IQ-tree | #main/A partition file ready for input into RAxML or IQ-tree | n/a |
|
| An occupancy file that summarizes the taxon occupancy per sequence | #main/An occupancy file that summarizes the taxon occupancy per sequence | n/a |
|
| ClustalW on input dataset(s): clustal | #main/ClustalW on input dataset(s): clustal | n/a |
|
| Concatenated fasta alignment file | #main/Concatenated fasta alignment file | n/a |
|
| Proteinortho on input dataset(s): orthology-groups | #main/Proteinortho on input dataset(s): orthology-groups | n/a |
|
| Proteinortho_extract_by_orthogroup | #main/Proteinortho_extract_by_orthogroup | n/a |
|
| Trimmed alignment. | #main/Trimmed alignment. | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| extracted_ORFs | #main/extracted_ORFs | n/a |
|
| fasta_header_cleaned | #main/fasta_header_cleaned | n/a |
|
| funannotate_predicted_proteins | #main/funannotate_predicted_proteins | n/a |
|
| headers_shortened | #main/headers_shortened | n/a |
|
| proteomes_to_one_file | #main/proteomes_to_one_file | n/a |
|
| repeat_masked | #main/repeat_masked | n/a |
|
| sample_names_to_headers | #main/sample_names_to_headers | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:10 by Helena Rasche
Added/updated 4 files
Open
master17df822
2.0 (earliest) Created 25th Jun 2024 at 11:17 by Helena Rasche
Added/updated 4 files
Frozen
2.00a6a734
Creators and Submitter
Views: 179 Downloads: 75
Created: 25th Jun 2024 at 11:17
Last updated: 25th Jun 2024 at 11:17
AttributionsNone
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