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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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About meaning of -c parameter #41

Closed hungweichen0327 closed 4 years ago

hungweichen0327 commented 4 years ago

Dear community,

The -c parameter is used to generate the consensus sequence. And I still not understand the meaning of value with -c parameter. For example:

smartdenovo.pl -c 1 -J 1000 -k ${k} -p Crystal_c1s1_${k}mer ../Crystal_all_1kb.correctedReads.fasta > Crystal_v1.8_1kb_17mer.mak

I don't know what's the difference if I changed -c 1 to -c 2, or -c 5. (Any more value? like -2?) So far I have Nanopore corrected reads, and I want to use Smartdenovo to do assembly.

Thank you.

ruanjue commented 4 years ago

The same, -c bool_value, zero or non-zero.

hungweichen0327 commented 4 years ago

Thank you for the fast reply. I got it!