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03_soapdenovo_wgs.config
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03_soapdenovo_wgs.config
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# maximal read length
max_rd_len=100
[LIB]
# average insert size
avg_ins=400
# if sequence needs to be reversed
reverse_seq=0
asm_flags=3
# use only first 50 bps of each read
#rd_len_cutoff=50
# in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (default 3)
pair_num_cutoff=3
# minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
# fastq file for read 1
q1=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819794.trim_1P.fastq.gz
# fastq file for read 2 always follows fastq file for read 1
q2=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819794.trim_2P.fastq.gz
# fastq file for read 3
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819794.trim_1U.fastq.gz
# fastq file for read 4
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819794.trim_2U.fastq.gz
[LIB]
# average insert size
avg_ins=800
# if sequence needs to be reversed
reverse_seq=0
asm_flags=3
# use only first 50 bps of each read
#rd_len_cutoff=50
# in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (default 3)
pair_num_cutoff=3
# minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
# fastq file for read 5
q1=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819795.trim_1P.fastq.gz
# fastq file for read 6
q2=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819795.trim_2P.fastq.gz
# fastq file for read 7
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819795.trim_1U.fastq.gz
# fastq file for read 8
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819795.trim_2U.fastq.gz
[LIB]
# average insert size
avg_ins=9000
# if sequence needs to be reversed
reverse_seq=1
asm_flags=2
# use only first 50 bps of each read
#rd_len_cutoff=50
# in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (default 3)
pair_num_cutoff=5
# minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
# fastq file for read 9
q1=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819796.trim_1P.fastq.gz
# fastq file for read 10
q2=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819796.trim_2P.fastq.gz
# fastq file for read 11
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819796.trim_1U.fastq.gz
# fastq file for read 12
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819796.trim_2U.fastq.gz
[LIB]
# average insert size
avg_ins=175
# if sequence needs to be reversed
reverse_seq=0
asm_flags=3
# use only first 50 bps of each read
#rd_len_cutoff=50
# in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (default 3)
pair_num_cutoff=3
# minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
# fastq file for read 13
q1=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819797.trim_1P.fastq.gz
# fastq file for read 14
q2=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819797.trim_2P.fastq.gz
# fastq file for read 15
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819797.trim_1U.fastq.gz
# fastq file for read 16
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819797.trim_2U.fastq.gz
[LIB]
# average insert size
avg_ins= 3000
# if sequence needs to be reversed
reverse_seq=1
asm_flags=2
# use only first 50 bps of each read
#rd_len_cutoff=50
# in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (default 3)
pair_num_cutoff=5
# minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
# fastq file for read 17
q1=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819798.trim_1P.fastq.gz
# fastq file for read 18
q2=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819798.trim_2P.fastq.gz
# fastq file for read 19
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819798.trim_1U.fastq.gz
# fastq file for read 20
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819798.trim_2U.fastq.gz
[LIB]
# average insert size
avg_ins= 5500
# if sequence needs to be reversed
reverse_seq=1
asm_flags=2
# use only first 50 bps of each read
#rd_len_cutoff=50
# in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (default 3)
pair_num_cutoff=5
# minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
# fastq file for read 21
q1=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819799.trim_1P.fastq.gz
# fastq file for read 22
q2=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819799.trim_2P.fastq.gz
# fastq file for read 23
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819799.trim_1U.fastq.gz
# fastq file for read 24
q=/home/annaaskl/genome_analysis/data/raw_data/sel2/wgs_data/sel2_SRR5819799.trim_2U.fastq.gz