Hi,
I am trying to assemble a genome with nanopore reads using necat.pl assemble config.txt command.
The predicted genome size is about 700 Mb, and I am using more than 19 million reads as input.
Although I have set the POLISHING_STEP flag as true in the config file, the only output I get is the contigs.fasta in the 4-fsa directory. Is there any reason why the polishing step is not working?
Moreover, the assembly reconstruction is taking more than 50 hours (with 20 threads set in the config file). Is there any way to speed up this step?
Thank you in advance for your help!
Hi,
I am trying to assemble a genome with nanopore reads using necat.pl assemble config.txt command.
The predicted genome size is about 700 Mb, and I am using more than 19 million reads as input.
Although I have set the POLISHING_STEP flag as true in the config file, the only output I get is the contigs.fasta in the 4-fsa directory. Is there any reason why the polishing step is not working?
Moreover, the assembly reconstruction is taking more than 50 hours (with 20 threads set in the config file). Is there any way to speed up this step?
Thank you in advance for your help!