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: mapsource: fq_inputcategory: outputoptional: {}pattern: ./*.bam- bfa_output
BFA Index name
type: singlecategory: otheroptional: {}pattern: {}- bfq_output
bfq files - forward files
type: mapsource: fq_inputcategory: outputoptional: {}pattern: ./*.bfq- fa_input
- directory with reference fasta file name
- fq_input
- fastq input files
- map_output
maq map output files
type: mapsource: fq_inputcategory: outputoptional: {}pattern: ./*.map
Parameters¶
- disable_sw
disable Smith-Waterman alignment
type: booleandefault: Falseoptional: True- extra_parameters
other parameters
type: stringdefault: ``optional: True- match_in_colorspace
match in the colorspace
type: booleandefault: Falseoptional: True- max_mismatch_qual_sum
maximum allowed sum of qualities of mismatches
type: integerdefault: 70optional: True- max_num_hits_out
number of mismatches in the first 24bp
type: integerdefault: 250optional: True- num_mismatch_24bp
number of mismatches in the first 24bp
type: integerdefault: 2optional: True- read_ref_diff_rate
rate of difference between reads and references
type: floatdefault: 0.001optional: True- trim_all_reads
trim all reads (usually not recommended)
type: booleandefault: Falseoptional: True
miscellaneous¶
- Backend
- ruff
- Author
- Mark Fiers, Yogini Idnani
- Creation date
- Wed Dec 02 17:06:48 2010
- Modification date
- unknown