#maximal read length
max_rd_len=100
[LIB]
#average insert size
avg_ins=200
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 100 bps of each read
rd_len_cutoff=100
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/path/**LIBNAMEA**/fastq1_read_1.fq
q2=/path/**LIBNAMEA**/fastq1_read_2.fq
#another pair of fastq file, read 1 file should always be followed by read 2 file
q1=/path/**LIBNAMEA**/fastq2_read_1.fq
q2=/path/**LIBNAMEA**/fastq2_read_2.fq
#a pair of fasta file, read 1 file should always be followed by read 2 file
f1=/path/**LIBNAMEA**/fasta1_read_1.fa
f2=/path/**LIBNAMEA**/fasta1_read_2.fa
#another pair of fasta file, read 1 file should always be followed by read 2 file
f1=/path/**LIBNAMEA**/fasta2_read_1.fa
f2=/path/**LIBNAMEA**/fasta2_read_2.fa
#fastq file for single reads
q=/path/**LIBNAMEA**/fastq1_read_single.fq
#another fastq file for single reads
q=/path/**LIBNAMEA**/fastq2_read_single.fq
#fasta file for single reads
f=/path/**LIBNAMEA**/fasta1_read_single.fa
#another fasta file for single reads
f=/path/**LIBNAMEA**/fasta2_read_single.fa
#a single fasta file for paired reads
p=/path/**LIBNAMEA**/pairs1_in_one_file.fa
#another single fasta file for paired reads
p=/path/**LIBNAMEA**/pairs2_in_one_file.fa
#bam file for single or paired reads, reads 1 in paired reads file should always be followed by reads 2
#    NOTE: If a read in bam file fails platform/vendor quality checks(the flag field 0x0200 is set), itself and it's paired read would be ignored.
b=/path/**LIBNAMEA**/reads1_in_file.bam
#another bam file for single or paired reads
b=/path/**LIBNAMEA**/reads2_in_file.bam
[LIB]
avg_ins=2000
reverse_seq=1
asm_flags=2
rank=2
# cutoff of pair number for a reliable connection (at least 5 for large insert size)
pair_num_cutoff=5
#minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
map_len=35
q1=/path/**LIBNAMEB**/fastq_read_1.fq
q2=/path/**LIBNAMEB**/fastq_read_2.fq
f1=/path/**LIBNAMEA**/fasta_read_1.fa
f2=/path/**LIBNAMEA**/fasta_read_2.fa
p=/path/**LIBNAMEA**/pairs_in_one_file.fa
b=/path/**LIBNAMEA**/reads_in_file.bam