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: map
source: input
category: output
optional: {}
pattern: ./*.sai

Parameters

best_hits_stop

stop searching when there are >INT equally best hits

type: integer
default: {}
optional: True
color_space

input sequences are in the color space

type: boolean
default: False
optional: True
db

bwa database to align against

type: string
default: {}
optional: False
edit_dist_missing_prob

max

type: float
default: {}
optional: True

gap_ext_max

type: integer
default: {}
optional: True
gap_ext_penalty

gap extension penalty

type: integer
default: {}
optional: True
gap_open_penalty

gap open penalty

type: integer
default: {}
optional: True
gap_opens_max

maximum number or fraction of gap opens

type: integer
default: {}
optional: True
log_gap_penalty_del

log-scaled gap penalty for long deletions

type: boolean
default: {}
optional: True
max_ext_long_del

maximum occurrences for extending a long deletion

type: integer
default: {}
optional: True
max_queue_entry

maximum entries in the queue

type: integer
default: {}
optional: True
mismatch_penalty

mismatch penalty

type: integer
default: {}
optional: True
no_indel_from_ends

do not put an indel within INT bp towards the ends

type: integer
default: {}
optional: True
non_iterative

non-iterative mode search for all n-difference hits (slow)

type: boolean
default: False
optional: True
quality_step

quality threshold for read trimming down to 35bp

type: integer
default: {}
optional: True
seed_len

Seed length

type: integer
default: {}
optional: True
seed_max_diff

Maximum differences in the seed

type: integer
default: {}
optional: True
thread_num

number of threads

type: integer
default: {}
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers, Yogini Idnani
Creation date
Wed Nov 10 07:56:48 2010
Modification date
unknown