maq_se

Generate alignments in SAM format given single end reads using Maq.

Commands

clean
Remove all job data, not the Moa job itself
run
run maq’s fasta2bfa, fastq2bfq and map.

Filesets

bam_output

bam alignment output file

type: map
source: fq_input
category: output
optional: {}
pattern: ./*.bam
bfa_output

BFA Index name

type: single
category: other
optional: {}
pattern: {}
bfq_output

bfq files - forward files

type: map
source: fq_input
category: output
optional: {}
pattern: ./*.bfq
fa_input
directory with reference fasta file name
fq_input
fastq input files
map_output

maq map output files

type: map
source: fq_input
category: output
optional: {}
pattern: ./*.map

Parameters

disable_sw

disable Smith-Waterman alignment

type: boolean
default: False
optional: True
extra_parameters

other parameters

type: string
default: ``
optional: True
match_in_colorspace

match in the colorspace

type: boolean
default: False
optional: True
max_mismatch_qual_sum

maximum allowed sum of qualities of mismatches

type: integer
default: 70
optional: True
max_num_hits_out

number of mismatches in the first 24bp

type: integer
default: 250
optional: True
num_mismatch_24bp

number of mismatches in the first 24bp

type: integer
default: 2
optional: True
read_ref_diff_rate

rate of difference between reads and references

type: float
default: 0.001
optional: True
trim_all_reads

trim all reads (usually not recommended)

type: boolean
default: False
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers, Yogini Idnani
Creation date
Wed Dec 02 17:06:48 2010
Modification date
unknown