maq_match_pair

MAQ paired ends mapper

Map paired ends to a reference sequence using MAQ

Commands

clean

Remove all job data, not the Moa job itself, note that this must be implemented by the template.

run

no help defined

Parameters

forward_suffix

Suffix of each forward filename - recognize forward files this way. Note this is not a regular extension, no . is assumed between the filename & suffix

type: string

default: _f.bfq

optional: True

maxdist

max outer distance for a (non RF) readpair. This applies to illumina matepairs - i.e. short inserts

type: integer

default: 250

optional: True

read_dir

directory containing the forward reads

type: string

default: ``

optional: False

reference

Reference bfa file to map the reads to

type: string

default: ``

optional: False

reverse_suffix

suffix of reverse files

type: string

default: _r.bfq

optional: True

RF_maxdist

max outer distance for an RF readpair (corresponds to the -A parameter). This applies to long insert illumina pairs

type: integer

default: 15000

optional: True

miscellaneous

Backend

gnumake

Author

Mark Fiers

Creation date

Wed Nov 10 07:56:48 2010

Modification date

Wed Nov 10 07:56:48 2010