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