Parameters setting problem

ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

GNU General Public License v3.0

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Parameters setting problem #121

Closed Sparkle-27 closed 5 years ago

Sparkle-27 commented 5 years ago

Hi Ruanjue I found a problem when I assembling with 100x corrected reads using canu, numerous reads will be missed loading using default -X [50]. The script I used as following:

$wtdbg2 -t ${Threads} -x corrected -g 2.5g -L 5000 -i ${RawReads} -fo ${output}

Do you have any suggestion about how to assembly the 2.5g genomeSize with 100x corrected reads? Thanks in advance!

ruanjue commented 5 years ago

-X 100 will selecting 100X reads from input.

wtdbg2 -t 64 -x ccs -g 2.5g -X 100 -i reads.fa -fo dbg

ruanjue commented 5 years ago

I my experience, shorter pacbio reads contributed little to wtdbg's assembly.

Please see wtdbg2 --help , selecting longest subread.

 -L <int>    Choose the longest subread and drop reads shorter than <int> (5000 recommended for PacBio) [0]
             Negative integer indicate tidying read names too, e.g. -5000.