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aquaskyline / SOAPdenovo2

Next generation sequencing reads de novo assembler.
GNU General Public License v3.0
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how to choose the kmer number for the genome assembly. #33

Closed fhu2008-tio closed 6 years ago

fhu2008-tio commented 6 years ago

Hi, when I run graphy and contig, different Kmer results differernt contig size, eg. kmer25=110M, kmer41=58M, does it normal? which number of kmer should be choose for the following analysis???

my illunima date 350bp, PE150,

example.config max_rd_len=150 [LIB] avg_ins=350 reverse_seq=0 asm_flags=1 rank=1 f1=/home/workplace/soapdenovo_350/cleanreads/350.1.fasta f2=/home/workplace/soapdenovo_350/cleanreads/350.2.fasta

cchd0001 commented 6 years ago

Hi , @fhu2008-tio

The best K changed for different data . You need to try more K and find the best. Since you read is long enough ,feel free to try bigger K , like 83 or even bigger . :-)

Hope this can help.