Description

cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

fasta{:bash}

:file

Multiple sequence alignment (unzipped)

*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}

Output

name:type
description
pattern

consensus{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.fa{:bash}

:file

Consensus sequence calculated from multiple sequence alignment

*.fa

versions_emboss{:bash}

${task.process}{:bash}

:string

The name of the process

emboss{:bash}

:string

The name of the tool

cons -version 2>&1 | sed "s/EMBOSS://"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

emboss{:bash}

:string

The name of the tool

cons -version 2>&1 | sed "s/EMBOSS://"{:bash}

:eval

The expression to obtain the version of the tool

Tools

maintainer
Github user Joon-Klaps
get in touch
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