bwa_aln¶
Use BWA to align a set of fastq reads against a db
Commands¶
- clean
- Remove all job data, not the Moa job itself, note that this must be implemented by the template.
- run
- run bwa aln
Filesets¶
- input
- Fastq input files
output
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.sai
Parameters¶
- best_hits_stop
stop searching when there are >INT equally best hits
type: integerdefault: {}optional: True- color_space
input sequences are in the color space
type: booleandefault: Falseoptional: True- db
bwa database to align against
type: stringdefault: {}optional: False- edit_dist_missing_prob
max
type: floatdefault: {}optional: True
gap_ext_max
type: integerdefault: {}optional: True
- gap_ext_penalty
gap extension penalty
type: integerdefault: {}optional: True- gap_open_penalty
gap open penalty
type: integerdefault: {}optional: True- gap_opens_max
maximum number or fraction of gap opens
type: integerdefault: {}optional: True- log_gap_penalty_del
log-scaled gap penalty for long deletions
type: booleandefault: {}optional: True- max_ext_long_del
maximum occurrences for extending a long deletion
type: integerdefault: {}optional: True- max_queue_entry
maximum entries in the queue
type: integerdefault: {}optional: True- mismatch_penalty
mismatch penalty
type: integerdefault: {}optional: True- no_indel_from_ends
do not put an indel within INT bp towards the ends
type: integerdefault: {}optional: True- non_iterative
non-iterative mode search for all n-difference hits (slow)
type: booleandefault: Falseoptional: True- quality_step
quality threshold for read trimming down to 35bp
type: integerdefault: {}optional: True- seed_len
Seed length
type: integerdefault: {}optional: True- seed_max_diff
Maximum differences in the seed
type: integerdefault: {}optional: True- thread_num
number of threads
type: integerdefault: {}optional: True
miscellaneous¶
- Backend
- ruff
- Author
- Mark Fiers, Yogini Idnani
- Creation date
- Wed Nov 10 07:56:48 2010
- Modification date
- unknown