Hello everyone,
I am new to assembly and I have a syntax question to ask:
This is an example contig file as given on https://github.com/aquaskyline/SOAPdenovo2
In the [LIB] section, we already specify parameters such as avg_ins, reverse_seq, asm_flags, rank etc then why do we again define the limits outside the [LIB] at the end of the file? Are those maximum values of these parameters?
I tried to find this in the documentation but couldnt get any information
I am new to assembly and I have a syntax question to ask:
This is an example contig file as given on https://github.com/aquaskyline/SOAPdenovo2
In the [LIB] section, we already specify parameters such as avg_ins, reverse_seq, asm_flags, rank etc then why do we again define the limits outside the [LIB] at the end of the file? Are those maximum values of these parameters?
I tried to find this in the documentation but couldnt get any information
Code:
#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 [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
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