Recommended parameters for coverage titration?

ruanjue / wtdbg2

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

GNU General Public License v3.0

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Recommended parameters for coverage titration? #117

Closed adigenova closed 5 years ago

adigenova commented 5 years ago

Hi, I'm trying to determine the coverage peak of wtdbg2 on a human genome. I'm using ONT data at the following coverage:

10X, 15X, 20X, 25X, 30X, 35X, 40X, 45X, 50X

What parameters should I tune to maximize performance at each coverage?.

Thank in advance. Best Alex

ruanjue commented 5 years ago

I am afraid <20X won't work. If you are assembling low coverage data, please also try realignment option -R to get more accurate alignments. Please note that wtdbg2 has an default option -X50 to select 50X reads.

Best, Jue

adigenova commented 5 years ago

Great!!! thanks.