Newbler --- classify many reads as Repeat

[NSTbioinformatics]

Hello,

Newbler classified many reads as Repeat and throws them away from the assembly. In my analysis 24% reads are Repeats.

Does anyone know how to switch off this function?

Thank you vey much.

[jvhaarst]

In short : You can't.

We had Newbler throwing away 50% of the reads, so we had a look at CABOG, which in our case looks to be the better choice.

[cjf]

I don't think it's a big problem any way. If your sequenced species had several WGD, you do expect large number of repeats in the genome. BTW, have you looked at the latest version of GAP5? It sounds quite promissing.