autohagfish

Automatically run bowtie & hagfish combined

Run the preparatory steps for hagfish

Commands

clean
remove all Hagfish files
finish
finish up - find gaps - combine plots - create a report
run
Run hagfish

Filesets

fasta

fasta sequence of the reference

type: single
category: prerequisite
optional: False
pattern: {}
fw_fq
forward fq input
outbase

basename for output files

type: map
source: fw_fq
category: output
optional: True
pattern: ./*
rev_fq

reverse fq input

type: map
source: fw_fq
category: input
optional: True
pattern: */*2.fq

Parameters

max_ok

Maximal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate

type: int
default: 0
optional: True
min_ok

Minimal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate

type: int
default: 0
optional: True
threads

no threads to use

type: integer
default: 8
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers
Creation date
Tue Mar 29 16:34:19 2011
Modification date
Thu, 19 May 2011 20:49:04 +1200