Reproducibility of results

ruanjue / wtdbg2

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

GNU General Public License v3.0

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Reproducibility of results #80

Closed trichoptera closed 5 years ago

trichoptera commented 5 years ago

Dear Jue Ruan,

I was running wtdbg2 on the same data set with the same parameters but got slightly different assembly statistics. Is this possible? Is there an explanation for this? Could you please also explain why wtdbg2 may produce an assembly smaller than the true genome when using Nanopore data?

Thank you!

ruanjue commented 5 years ago

The step of selecting vertices from read alignments is multi-threads, thusly cause very few runtime depended differences.

wtdbg2 tends to collapse haplotypes/repeats as in de Bruijn graph. QUAST always give the lowest duplication rate to wtdbg2.

Jue

trichoptera commented 5 years ago

Thank you for your answer!