modules/proteinortho

Proteinortho is a tool to detect orthologous genes within different species.

orthologyco-orthologyhomologysequence similarityspectral clusteringcomparative genomicsgenomics

https://github.com/nf-core/modules/[...]/modules/nf-core/proteinortho

Description

Proteinortho is a tool to detect orthologous genes within different species.

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:'test' ]

`fasta_files:file`

Input fasta files (proteomes or transcriptomes), at least 2 are needed

*.{fa,fasta,faa,fna,fn}

Output

name:type

description

pattern

`orthologgroups`

`meta:file`

Orthology table

*.proteinortho.tsv

`${meta.id}.proteinortho.tsv:file`

Orthology table

*.proteinortho.tsv

`orthologgraph`

`meta:file`

Orthology graph

*.proteinortho-graph

`${meta.id}.proteinortho-graph:file`

Orthology graph

*.proteinortho-graph

`blastgraph`

`meta:file`

BLAST graph

*.blast-graph

`${meta.id}.blast-graph:file`

BLAST graph

*.blast-graph

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

proteinortho
GPL v3

Proteinortho is a tool to detect orthologous genes within different species.

gitlab.com/paulklemm_PHD/proteinortho gitlab.com/paulklemm_PHD/proteinortho#proteinortho https://gitlab.com/paulklemm_PHD/proteinortho 10.3389/fbinf.2023.1322477

modules/proteinortho

Description

Input

`meta:map`

`fasta_files:file`

Output

`orthologgroups`

`meta:file`

`${meta.id}.proteinortho.tsv:file`

`orthologgraph`

`meta:file`

`${meta.id}.proteinortho-graph:file`

`blastgraph`

`meta:file`

`${meta.id}.blast-graph:file`

`versions`

`versions.yml:file`

Tools

proteinortho
GPL v3

maintainer

get in touch

modules/proteinortho

Description

Input

meta:map

fasta_files:file

Output

orthologgroups

meta:file

${meta.id}.proteinortho.tsv:file

orthologgraph

meta:file

${meta.id}.proteinortho-graph:file

blastgraph

meta:file

${meta.id}.blast-graph:file

versions

versions.yml:file

Tools

proteinortho GPL v3

maintainer

get in touch

`meta:map`

`fasta_files:file`

`orthologgroups`

`meta:file`

`${meta.id}.proteinortho.tsv:file`

`orthologgraph`

`meta:file`

`${meta.id}.proteinortho-graph:file`

`blastgraph`

`meta:file`

`${meta.id}.blast-graph:file`

`versions`

`versions.yml:file`

proteinortho
GPL v3