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: map
source: fq_input
category: output
optional: {}
pattern: ./*.aln

output_bam

type: map
source: fq_input
category: output
optional: {}
pattern: ./*.bam

Parameters

algorithm_colour_space

true -> colour space, false -> NT space

type: boolean
default: False
optional: True
avg_mism_qual

Specifies the average mismatch quality

type: integer
default: 10
optional: True
extra_params_localalign

Any extra parameters for the localalign command

type: string
default: ``
optional: True
extra_params_match

Any extra parameters for the match command

type: string
default: ``
optional: True
extra_params_postprocess

Any extra parameters for the postprocess command

type: string
default: ``
optional: True
min_mapping_qual

Specifies to remove low mapping quality alignments

type: integer
default: -2147483648
optional: True
min_norm_score

Specifies to remove low (alignment) scoring alignments

type: integer
default: -2147483648
optional: True
output_format

0 - BAF, 1 - SAM

type: integer
default: 1
optional: True
paired_opp_strands

Specifies that paired reads are on opposite strands

type: boolean
default: False
optional: True
pairing_std_dev

Specifies the pairing distance standard deviation to examine when recuing

type: float
default: 2.0
optional: True
print_params

print program parameters

type: boolean
default: False
optional: True
thread_num

Specifies the number of threads to use

type: integer
default: 1
optional: True
timing_information

specifies output timing information

type: boolean
default: True
optional: True
ungapped_aln

Do ungapped local alignment

type: boolean
default: False
optional: True
ungapped_pairing_rescue

Specifies that ungapped pairing rescue should be performed

type: boolean
default: False
optional: True
unpaired_reads

True value specifies that pairing should not be performed

type: boolean
default: False
optional: True
usage_summary

Display usage summary (help)

type: boolean
default: False
optional: True
which_strand

0 - consider both strands, 1 - forwards strand only, 2 - reverse strand only

type: integer
default: 0
optional: True

miscellaneous

Backend
ruff
Author
Yogini Idnani, Mark Fiers
Creation date
Wed Feb 15 10:06:48 2011
Modification date
unknown