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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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What if users use corrected reads instead of raw long-reads? #179

Closed DomeJoyce closed 4 years ago

DomeJoyce commented 4 years ago

Hello there, i was wandering if the use of already corrected reads can produce biased results on wtdbg2 assembly, since in the manual you declare " Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.". I really appreciate your work and i'm using for a PacBio (only) genome assembly. Many thanks

ruanjue commented 4 years ago

wtdbg2 -x ccs will help.

tauanajc commented 4 years ago

Hi there Jue Ruan, Given the same quote that DomeJoyce mentioned above, it is not clear to me what the ideal input files are. I am using nanopore data, and I know there is a preset for that. My question is, is the recommendation to use raw reads that were base called without any quality filtering, or should we filter for quality during basecalling, and then use the base called raw data as input to wtdbg2? Thanks!

ruanjue commented 4 years ago

In fact, I haven't try filtering. But I think it will help.