Jue Ruan

It should be a complicate genome, try tune parameters `-R`, `--aln-dovetail 0` and others referred in issues.

The minimal count of reads to support that two genomic regions are directly connected in order. On graph, the minimal count of reads to support a confident edge.

The first step is to check whether the polished contigs are more accurate using WGS short reads.

So, the reason should be many repeats were collapsed in assembling, not the problem of wtpoa-cns. One option is to add `-R` to `wtdbg2`, which will be 2X slower. Another...

In wtdbg2 step, the assembly size was stated by uncorrected seqeunce length, usually will become smaller after wtpoa-cns.

If the genome size was correctly estimated and the genome was complicated, maybe there is no way. However, please find out some contigs that differed much in size between before...

wtdbg2 tends to collapse similar regions. For your case, please try increase '-s 0.5' to '-s 0.8' or others.

1, min_match: yes, you are right. 2, `--dp-penalty-gap` and `--dp-penalty-var` are not calculated in the same way with SW, they are just used to stop the tracing in sparse matrix...

Have a look at the `Quatiles` log message, like this ```txt Quatiles: 10% 20% 30% 40% 50% 60% 70% 80% 90% 95% 16 21 29 72 268 972 3329 11697...

```txt [Fri Feb 5 16:57:44 2021] - high frequency kmer depth is set to 16534 ``` Try to set `-K 2000` to speed it up.