newbler

Newbler

Run a simple, out of the box, newbler assembly. As an extra feature, this template automatically creates uniquely named links to the two main output fasta files (454AllContigs.fna, 454LargeContigs.fna). This is convenient for subsequence gather steps. The links are named after the directory.

Commands

clean

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

run

no help defined

Filesets

input

input SFF files

Parameters

largecontig_cutoff

min length of a contig in 454LargeContigs.fna

type: integer

default: ``

optional: True

library_name

A library identifier for this assembly. This is used to create an extra fasta file, named using this variable, that contain the generated contigs with their ids prepended with the library id.

type: string

default: $(shell echo `basename $(CURDIR) | sed “s/[ ////]//g” )`

optional: True

mid_configuration

Mid configuration file to use

type: file

default: ``

optional: True

mids

mids to use for this assembly

type: string

default: ``

optional: True

min_identity

Minimal overalp identity used during assembly

type: integer

default: ``

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