maq_pe

Generate alignments in SAM format given paired end reads using Maq.

Commands

clean
Remove all job data, not the Moa job itself
run
run maq’s fasta2bfa, fastq2bfq and map.

Filesets

bam_output

bam alignment output file

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

BFA Index name

type: single
category: other
optional: {}
pattern: {}
bfq_forward_output

bfq files - forward files

type: map
source: fq_forward_input
category: output
optional: {}
pattern: ./*_1.bfq
bfq_reverse_output

bfq files - reverse files

type: map
source: fq_forward_input
category: output
optional: {}
pattern: ./*_2.bfq
fa_input
directory with reference fasta file name
fq_forward_input
fastq input files directory - forward files
fq_reverse_input

fastq input files directory - reverse files

type: map
source: fq_forward_input
category: input
optional: {}
pattern: */*_2.fq
map_output

maq map output files

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

Parameters

disable_sw

disable Smith-Waterman alignment

type: boolean
default: False
optional: True
extra_parameters

Any extra parameters

type: string
default: ``
optional: True
first_read_len

length of the first read (<=127)s

type: integer
default: 0
optional: True
match_in_colorspace

match in the colorspace

type: boolean
default: False
optional: True
max_dist_read_pairs

max distance between two paired reads s

type: integer
default: 250
optional: True
max_dist_RF_read_pairs

max distance between two RF paired reads s

type: integer
default: 0
optional: True
max_mismatch_qual_sum

maximum allowed sum of qualities of mismatches

type: integer
default: 70
optional: True
max_num_hits_out

max number of hits to output. >512 for all 01 hits.

type: integer
default: 250
optional: True
num_mismatch_24bp

number of mismatches in the first 24bp

type: integer
default: 2
optional: True
read_ref_diff_rate

rate of difference between reads and references

type: float
default: 0.001
optional: True
sec_read_len

length of the second read (<=127)s

type: integer
default: 0
optional: True
trim_all_reads

trim all reads (usually not recommended)

type: boolean
default: False
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers, Yogini Idnani
Creation date
Wed Dec 03 17:06:48 2010
Modification date
unknown