default_param_ver1.1.0.txt

# minimum length of the soft-clipped region
clipping_size = 5

# threshold of average base quality of soft clipped region
baseQthreshold = 60

# minimum number of soft-clipped reads required
soft_clip_map_sum = 3

# minimum number of soft-clipped reads required at each direction of the breakpoint
support_soft_clip_map = 2

# coverage of input data
coverage = 30

# profile threshold
profile_cutoff = 0.90

# overlap reads percentage of the breakpoint
overlapFilterRatio = 0.1

# flag for identifying MGEs using BLAST search
# 1 for searching; 0 for not searching
blast_flag = 1

# maximum length of upstream/downstream regions for finding singly-mapped reads
sm_range = 500

# path to the MGE database file for BLAST search
MGE_DB_path = /path/to/fasta/sample_MGE_DB.fasta

# similarity threshold to filter BLAST results
similarity_cutoff = 90.0

# alignment length threshold to filter BLAST results
align_length_cutoff = 70

# flag for assembling unmapped reads using SOAP denvo2
# 1 for searching; 0 for not searching
assembly_flag = 1

#average insert length for SOAPdenovo2 config file
avg_ins= 400

#maximum read length for SOAPdenovo2 config file
max_rd_len= 101

#contig length cutoff
contig_len_cutoff = 500

# minimum number of mapped reads to each contig
contig_map_read_cutoff=10

#number of threads
numOfThread = 32