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: mapsource: rds_inputcategory: outputoptional: Truepattern: ./*.sam- output_bam
output files
type: mapsource: rds_inputcategory: outputoptional: Truepattern: ./*.bam- output_log
output log file
type: mapsource: rds_inputcategory: outputoptional: {}pattern: ./*.log.txt- rds_input
- rds (preprocessed) input files
- sfx_input
- sfx array lookup file
Parameters¶
- color_space
process for colorspace (SOLiD)
type: booleandefault: Falseoptional: True- extra_params
any extra parameters
type: stringdefault: ``optional: True- help
print this help and exit
type: booleandefault: Falseoptional: True- max_Ns
maximum number of intermediate N’s in reads before treating read as unalignable
type: integerdefault: 1optional: True- max_pair_len
accept paired end alignments with apparent length of at most this
type: integerdefault: 300optional: True- min_pair_len
accept paired end alignments with apparent length of at least this
type: integerdefault: 100optional: True- no_multireads
do not accept multiple reads aligning to the same loci
type: booleandefault: Falseoptional: 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: integerdefault: 0optional: True- pe_mode
0 - none, 1 - paired ends with recover orphan ends, 2 - paired end no orphan recovery
type: integerdefault: 0optional: True- quality
fastq quality scoring- 0 - sanger, 1m - Illumina 1.3+, 2 - Solexa < 1.3, 3 - Ignore quality
type: integerdefault: 3optional: True- thread_num
number of processing threads (0 sets threads to number of CPU cores)
type: integerdefault: 0optional: True- trim3
trim this number of bases from 3’ end of reads when loading raw reads
type: integerdefault: 0optional: True- trim5
trim this number of bases from 5’ end of reads when loading raw reads
type: integerdefault: 0optional: True- version
print version information and exit
type: booleandefault: Falseoptional: True
miscellaneous¶
- Backend
- ruff
- Author
- Mark Fiers, Yogini Idnani
- Creation date
- Wed Nov 10 07:56:48 2010
- Modification date
- unknown