bfast_aln¶
Generate bam format alignments using bfast
Commands¶
- clean
- Remove all job data, not the Moa job itself
- run
- run bfast match, localalign, postprocess commands
Filesets¶
- fa_input
- fasta input file
- fq_input
- fastq input files
output_aln
type: mapsource: fq_inputcategory: outputoptional: {}pattern: ./*.aln
output_bam
type: mapsource: fq_inputcategory: outputoptional: {}pattern: ./*.bam
Parameters¶
- algorithm_colour_space
true -> colour space, false -> NT space
type: booleandefault: Falseoptional: True- avg_mism_qual
Specifies the average mismatch quality
type: integerdefault: 10optional: True- extra_params_localalign
Any extra parameters for the localalign command
type: stringdefault: ``optional: True- extra_params_match
Any extra parameters for the match command
type: stringdefault: ``optional: True- extra_params_postprocess
Any extra parameters for the postprocess command
type: stringdefault: ``optional: True- min_mapping_qual
Specifies to remove low mapping quality alignments
type: integerdefault: -2147483648optional: True- min_norm_score
Specifies to remove low (alignment) scoring alignments
type: integerdefault: -2147483648optional: True- output_format
0 - BAF, 1 - SAM
type: integerdefault: 1optional: True- paired_opp_strands
Specifies that paired reads are on opposite strands
type: booleandefault: Falseoptional: True- pairing_std_dev
Specifies the pairing distance standard deviation to examine when recuing
type: floatdefault: 2.0optional: True- print_params
print program parameters
type: booleandefault: Falseoptional: True- thread_num
Specifies the number of threads to use
type: integerdefault: 1optional: True- timing_information
specifies output timing information
type: booleandefault: Trueoptional: True- ungapped_aln
Do ungapped local alignment
type: booleandefault: Falseoptional: True- ungapped_pairing_rescue
Specifies that ungapped pairing rescue should be performed
type: booleandefault: Falseoptional: True- unpaired_reads
True value specifies that pairing should not be performed
type: booleandefault: Falseoptional: True- usage_summary
Display usage summary (help)
type: booleandefault: Falseoptional: True- which_strand
0 - consider both strands, 1 - forwards strand only, 2 - reverse strand only
type: integerdefault: 0optional: True
miscellaneous¶
- Backend
- ruff
- Author
- Yogini Idnani, Mark Fiers
- Creation date
- Wed Feb 15 10:06:48 2011
- Modification date
- unknown