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Old 08-19-2015, 01:37 AM   #1
Niranjanks
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Location: India

Join Date: Aug 2015
Posts: 11
Default Config file for soapdenovo2

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

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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Old 08-19-2015, 04:27 AM   #2
Linnea
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Posts: 23
Default

It's not outside [LIB], it's a second library that is defined! So for every library you have, you start with a line "[LIB]", and then list all the parameters (specific for each library).
In the example there is one paired end library and one mate-pair library.

Linnéa
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Old 08-19-2015, 08:40 PM   #3
Niranjanks
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Location: India

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Posts: 11
Default

Thanks a lot Linnéa!

That explains it nicely and now I also understand the 'Library rank'.
Thank you again
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