soapdenovo

配置文件中的=号两边不能有空格，否则会报错

SOAPdenovo-63mer_v2.0 all -s TongJiN2.config -p 25 -K 63 -d 1 -R  -F -o Lily_2 1>ass.log 2>ass.err

-s config file

-o prefix of output file name

-K kmer size

-p number of cpu to use

-d no larger than this value will be deleted

-R resolve repeats by reads

-F fill gaps in scaffold

-M <int>   mergeLevel(min 0, max 3): the strength of merging similar sequences during contiging, [1]

-L <int>       minContigLen: shortest contig for scaffolding, [K+2]

asm_flags
This indicator decides in which part(s) the reads are used. It takes value
1(only contig assembly), 2 (only scaffold assembly), 3(both contig and scaffold
assembly), or 4 (only gap closure).

rank
It takes integer values and decides in which order the reads are used for
scaffold assembly. Libraries with the same "rank" are used at the
same time during scaffold assembly.