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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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Nanopore sequence commands #44

Closed bioramg closed 4 years ago

bioramg commented 4 years ago

Hi, I would like to assemble the nanopore plant mitochondrial genome sequence using SMARTdenonovo. But I could not find any commands to run this data. Could you please give commands for the same.

Thank you.

ruanjue commented 4 years ago

https://github.com/ruanjue/smartdenovo#getting-started Try the standard commands.

bioramg commented 4 years ago

Thank you for quick reply.

/path/to/smartdenovo/smartdenovo.pl -p prefix -c 1 reads.fa > prefix.mak make -f prefix.mak

what does mean by -p, prefix.mak, and make -f prefix.mak?

bioramg commented 4 years ago

could you please give an example for nanopore assembly? Sorry to ask you. I am a very beginner.

ruanjue commented 4 years ago 
/path/to/smartdenovo/smartdenovo.pl -p asm01 -c 1 ont_reads.fa > prefix.mak
make -f prefix.mak
bioramg commented 4 years ago

Thank you so much