prefix.dmo.lay.utg and contig.fasta

[pengbo233]

Dear community, The -c parameter is used to generate the consensus sequence，but it is too slow. Can I use prefix.dmo.lay.utg as the final contig.fasta ？

Thank you.

[ruanjue]

I am afraid not, the consensus step is highly required, also plus following polishing with other tools.

[pengbo233]

[Wed Jun 24 01:15:19 2020] output 14374 independent unitigs [Wed Jun 24 01:15:29 2020] Done wtcns -t 60 prefix.dmo.lay > prefix.dmo.cns 2> prefix.dmo.cns.log 31M Jun 28 07:53 prefix.dmo.cns 23K Jun 24 01:15 work.sh.o2700188 3.5G Jun 24 01:15 prefix.dmo.lay.utg.dup 295M Jun 24 01:15 prefix.dmo.lay.lnk 3.8G Jun 24 01:15 prefix.dmo.lay.utg 9.9G Jun 24 01:15 prefix.dmo.lay.dup 44G Jun 24 01:15 prefix.dmo.lay 76M Jun 24 01:10 prefix.dmo.lay.5.dot 85M Jun 24 01:10 prefix.dmo.lay.4.dot 96M Jun 24 01:09 prefix.dmo.lay.3.dot 482M Jun 24 01:09 prefix.dmo.lay.2.dot 34M Jun 24 01:09 prefix.dmo.lay.contained_reads 5.2G Jun 24 01:09 prefix.dmo.lay.1.dot 1.7M Jun 24 01:06 work.sh.e2700188 94M Jun 23 23:25 prefix.dmo.obt 0 Jun 23 20:35 prefix.dmo.ovl.contained 89G Jun 23 20:35 prefix.dmo.ovl

The output of this program is very slow. How can I improve the speed ？

[pengbo233]

I am afraid not, the consensus step is highly required, also plus following polishing with other tools.

The output of this program is very slow. How can I improve the speed ？ It costs 7 days finishing 90/14374, I am afraid it will cost 10000h，it is too long。

[pengbo233]

I am afraid not, the consensus step is highly required, also plus following polishing with other tools. Dear community， How can I choose parameters of smartdenovo/wtcns to improve the speed ? Thank you very much!

[ruanjue]

Unusually slow. Could you send me the first 10 sections, each beginning with >. ruanjue.big (AT) qq.com