Hi,
I'm now using SOAPdenovo to assemble a big genome(Illumina GAIIx data;avg insert 200bp;pair-end reads 150bp x 2 ).
From the software manual, I found there is a parameter called "map_len".
In the example from the software manual, the default map_len=32, when maximal read length = 50 and average insert size = 200). In my case, my PE read length = 150, so, should I increase the map_len value?
Does anyone know how to set up a suitable map_len value?
PS: An example.config from the software manual:
"
#maximal read length
max_rd_len=50
[LIB]
#average insert size
avg_ins=200
...
...
#minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
...
[LIB]
avg_ins=2000
...
...
#minimum aligned length to contigs for a reliable read location
#(default 35 for large insert size)
map_len=35
... "
I'm now using SOAPdenovo to assemble a big genome(Illumina GAIIx data;avg insert 200bp;pair-end reads 150bp x 2 ).
From the software manual, I found there is a parameter called "map_len".
In the example from the software manual, the default map_len=32, when maximal read length = 50 and average insert size = 200). In my case, my PE read length = 150, so, should I increase the map_len value?
Does anyone know how to set up a suitable map_len value?
PS: An example.config from the software manual:
"
#maximal read length
max_rd_len=50
[LIB]
#average insert size
avg_ins=200
...
...
#minimum aligned length to contigs for a reliable read location (default 32)
map_len=32
...
[LIB]
avg_ins=2000
...
...
#minimum aligned length to contigs for a reliable read location
#(default 35 for large insert size)
map_len=35
... "
Comment