preparing genomic data for phylogeny recostruction (GTN)

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
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

preparing genomic data for phylogeny recostruction (GTN)
Version 1

Inputs

Steps

Outputs

Version History

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

Creators

Additional credit

Submitter

preparing genomic data for phylogeny recostruction (GTN) Version 1

Inputs

Steps

Outputs

Version History

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

Creators

Additional credit

Submitter

Related items

preparing genomic data for phylogeny recostruction (GTN)
Version 1