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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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Plasmid problems #217

Closed davidvilanova closed 4 years ago

davidvilanova commented 4 years ago

Hello, I have sequenced a plasmid with 50 tandem repeats (using nanopore) . It´s a lab plasmid used to produce a specific protein. The plasmid is 5Kb and tandem repeats(150nt) are also 5Kb so the overall estimated size is 10kb. The 5´prime of the plasmid is a vector and the 3´end also. Repeats are in between I have tried to assembly the plasmid using the following command:

-k 15 -p 0 -K 1000.049988 -A -S 4.000000 -s 0.050000 -g 0 -X 50.000000 -e 3 -L 5000

The final contig is too large and contains only a few of the expected tandem repeats. Mummer analysis does show that the plasmid does not match all the repeats. I also have the reference fasta sequence of the expected plasmid.

Is there a way to assembly such plasmid ?

ruanjue commented 4 years ago

Try increase the overlap length of alignment by -l 4096. Or plus -R option.

davidvilanova commented 4 years ago

Thanks, will give it a try