Dear folks,

I see "The `*-unitigs`

is the assembly without using any paired end or mate pair information, and the `*-contigs.fa`

is the next step, using paired end information. The `*-scaffolds.fa`

is your scaffolded contigs".

Here are the stats for my `-unitigs.fa`

, `-contigs.fa`

, and `-scaffolds.fa`

as below. On my understanding, the difference in total length between `*-unitigs.fa`

and `*-scaffolds.fa`

should be the number of Ns in my `-scaffolds.fa`

. Am I right? But, when I counted the number of Ns in `*-scaffolds.fa`

, there are only 509 Ns. What am I missing?

Also, on my understanding, the *-scaffolds.fa will use paired/mate pair information to join/scaffold the contigs together, right? If I am right, there should be 99 gaps filled with Ns in my `*-scaffolds.fa`. But I don't think there are 99 gaps of Ns in`

*-scaffolds.fa`. Where am I missing?

```
*-unitigs.fa
sequence #: 316 total length: 4678712 max length: 236245 N50: 34091 N90: 10761
*-contigs.fa
sequence #: 221 total length: 4776303 max length: 236245 N50: 40151 N90: 15786
*-scaffolds.fa
sequence #: 217 total length: 4776366 max length: 236245 N50: 40489 N90: 16196
```

Thank you so much!

PS: I just realized that I need to post question here. I am sorry if I posted it twice.

Best,

Xiaofei

Thank you so much! It really helps! :-)