preparing genomic data for phylogeny recostruction (GTN)
Version 1

Workflow Type: Galaxy

This 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. Test dataset: https://zenodo.org/record/6610704#.Ypn3FzlBw5k

Inputs

ID Name Description Type
Input genomes as collection Input genomes as collection n/a n/a
evidences evidences runtime parameter for tool Funannotate predict annotation n/a
evidences evidences runtime parameter for tool Funannotate predict annotation n/a
genemark genemark runtime parameter for tool Funannotate predict annotation n/a
genemark genemark runtime parameter for tool Funannotate predict annotation n/a
other_predictors other_predictors runtime parameter for tool Funannotate predict annotation n/a
other_predictors other_predictors runtime parameter for tool Funannotate predict annotation n/a
other_predictors other_predictors runtime parameter for tool Funannotate predict annotation n/a
other_predictors other_predictors runtime parameter for tool Funannotate predict annotation n/a
parameters parameters runtime parameter for tool Funannotate predict annotation n/a

Steps

ID Name Description
0 Input genomes as collection
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

Outputs

ID Name Description Type
outfile outfile n/a
output_masked_genome output_masked_genome n/a
output_log output_log n/a
output_table output_table n/a
output_repeat_catalog output_repeat_catalog n/a
annot_gbk annot_gbk n/a
aa_output aa_output n/a
nc_output nc_output n/a
out_file1 out_file1 n/a
output output n/a
blastgraph blastgraph n/a
proteinortho proteinortho n/a
proteinorthograph proteinorthograph n/a
busco_sum busco_sum n/a
busco_table busco_table n/a
busco_missing busco_missing n/a
out_file1 out_file1 n/a
listproteinorthograbproteins listproteinorthograbproteins n/a
out_file1 out_file1 n/a
output output n/a
dnd dnd n/a

Version History

Version 1 (earliest) Created 6th Jun 2022 at 15:05 by Miguel Roncoroni

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Miguel Roncoroni

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Views: 88

Created: 6th Jun 2022 at 15:05

Last used: 28th Jun 2022 at 23:41

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