Description of bug
Hello,
I try to find a gene whether is complete in my genome assembled by SPADES based on Illumina data. First I try spades.py -k 21,33,55,77,99 --isolate -t 46 --cov-cutoff auto -1 ${a}_1.rd.fastq -2 ${a}_2.rd.fastq -o output to generate a genome. Then I use blastn, and I get a complete gene sequence. Second, I try spades.py -k 17,33,43,55,77,99,111 --isolate -t 46 --cov-cutoff auto -1 ${a}_1.rd.fastq -2 ${a}_2.rd.fastq -o output to generate a genome. Then I use blastn, and I get a fragmental gene sequences in different 'NODE'. So is there any suggestion to choose the best k-mer combination when assemble a genome.
Looking forward your reply!
Best wishes
spades.log
if need
params.txt
if need
SPAdes version
v3.15.4
Operating System
MINT20
Python Version
Python 3.7.12
Method of SPAdes installation
conda
No errors reported in spades.log
Description of bug
Hello,
I try to find a gene whether is complete in my genome assembled by SPADES based on Illumina data. First I try
spades.py -k 21,33,55,77,99 --isolate -t 46 --cov-cutoff auto -1 ${a}_1.rd.fastq -2 ${a}_2.rd.fastq -o outputto generate a genome. Then I use blastn, and I get a complete gene sequence. Second, I tryspades.py -k 17,33,43,55,77,99,111 --isolate -t 46 --cov-cutoff auto -1 ${a}_1.rd.fastq -2 ${a}_2.rd.fastq -o outputto generate a genome. Then I use blastn, and I get a fragmental gene sequences in different 'NODE'. So is there any suggestion to choose the best k-mer combination when assemble a genome.Looking forward your reply!
Best wishes
spades.log
if need
params.txt
if need
SPAdes version
v3.15.4
Operating System
MINT20
Python Version
Python 3.7.12
Method of SPAdes installation
conda
No errors reported in spades.log