mummer¶

mummer

Run mummer between two sequences

Commands¶

clean: Remove all job data, not the Moa job itself, note that this must be implemented by the template.
run: Run mummer

base: base name for all generated files

type: {}

default: out

optional: True
breaklen: Set the distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200)

type: integer

default: 200

optional: True
genomecenter: genome center - used in the AGP file

type: {}

default: pflnz

optional: True
gff_source: GFF source field

type: {}

default: mumscaff

optional: True
linker: linker sequence for the merged output sequence

type: {}

default: NNNNNNCTAGCTAGCATGNNNNNN

optional: True
matchmode: use all matching fragments (max) or only unique matchers (mum)

type: set

default: mum

optional: True
mum_plot_raw: plot an alternative visualization where mummer does not attempt to put the sequences in the correct order

type: boolean

default: False

optional: True
organism: Organism name - used in the AGP file

type: {}

default: ``

optional: True
taxid: Taxonomy id - used in the AGP file

type: {}

default: ``

optional: True