glimmer3¶

Glimmer3

Predicts (prokaryotic) using glimmer3.

Commands¶

clean: Remove all job data, not the Moa job itself, note that this must be implemented by the template.
run: Glimmer3 is a open reading frame discovery program from the EMBOSS [[emboss]] package. It takes a set of input sequences and predicts all open reading frames. Additionally, this template converts the default output (predicted protein sequences) to GFF3.

cds: CDS output files from glimmer3

type: map

source: input

category: output

optional: True

pattern: cds/*.fasta
gff: GFF output files from glimmer3

type: map

source: input

category: output

optional: True

pattern: gff/*.gff
input: Directory with the input files for Glimmer3
output: Raw output files from glimmer3

type: map

source: input

category: output

optional: True

pattern: out/*.g3
pep: peptide output files from glimmer3

type: map

source: input

category: output

optional: True

pattern: pep/*.fasta

gene_len: Minimum gene length (glimmer3 -g/–gene_len)

type: integer

default: 110

optional: True
gff_source: source field to use in the gff. Defaults to “glimmer3”

type: string

default: glimmer3

optional: True
max_overlap: Maximum overlap, see the glimmer documentation for the -o or –max_olap parameter

type: integer

default: 50

optional: True
stop_codons: stop codons

type: {}

default: tag,tga,taa,nnn,tnn,ann,gnn,cnn

optional: True
treshold: treshold for calling a gene a gene (glimmer3 -t)

type: integer

default: 30

optional: True