soapdenovo_pe¶

Run Soapdenovo

Commands¶

fq_forward: fastq input files directory - forward
fq_reverse: fastq input files directory - reverse

type: map

source: fq_forward

category: input

optional: True

pattern: */*_2.fq
output: soap denovo output file

type: single

category: output

optional: True

pattern: output.scafSeq

avg_insert: library insert size

type: integer

default: 200

optional: {}
executable_not_used_anymore: which executable to use (SOAPdenovo-127mer, SOAPdenovo-31mer or SOAPdenovo-63mer)

type: {}

default: SOAPdenovo-31mer

optional: True
kmer: kmer size

type: integer

default: 31

optional: True
skip_config_file: skip automatic config file generation - if you skip this, make sure that you have a soap.config configuration file in the current directory

type: boolean

default: False

optional: True
threads: no threads to use

type: integer

default: 8

optional: True