kanga

use kanga to align short reads to a reference genome

Commands

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

Filesets

input_fasta
Fasta input file
output

output files

type: map
source: rds_input
category: output
optional: True
pattern: ./*.sam
output_bam

output files

type: map
source: rds_input
category: output
optional: True
pattern: ./*.bam
output_log

output log file

type: map
source: rds_input
category: output
optional: {}
pattern: ./*.log.txt
rds_input
rds (preprocessed) input files
sfx_input
sfx array lookup file

Parameters

color_space

process for colorspace (SOLiD)

type: boolean
default: False
optional: True
extra_params

any extra parameters

type: string
default: ``
optional: True
help

print this help and exit

type: boolean
default: False
optional: True
max_Ns

maximum number of intermediate N’s in reads before treating read as unalignable

type: integer
default: 1
optional: True
max_pair_len

accept paired end alignments with apparent length of at most this

type: integer
default: 300
optional: True
min_pair_len

accept paired end alignments with apparent length of at least this

type: integer
default: 100
optional: True
no_multireads

do not accept multiple reads aligning to the same loci

type: boolean
default: False
optional: True
out_format

0 - CSV loci only, 1 - CSV loci + match sequence, 2 - CSV loci + read sequence, 3 - CSV loci + read + match sequence, 4 - UCSC BED, 5 - SAM format

type: integer
default: 0
optional: True
pe_mode

0 - none, 1 - paired ends with recover orphan ends, 2 - paired end no orphan recovery

type: integer
default: 0
optional: True
quality

fastq quality scoring- 0 - sanger, 1m - Illumina 1.3+, 2 - Solexa < 1.3, 3 - Ignore quality

type: integer
default: 3
optional: True
thread_num

number of processing threads (0 sets threads to number of CPU cores)

type: integer
default: 0
optional: True
trim3

trim this number of bases from 3’ end of reads when loading raw reads

type: integer
default: 0
optional: True
trim5

trim this number of bases from 5’ end of reads when loading raw reads

type: integer
default: 0
optional: True
version

print version information and exit

type: boolean
default: False
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers, Yogini Idnani
Creation date
Wed Nov 10 07:56:48 2010
Modification date
unknown