[question] combine with medaka or not?
JWDebler opened this issue · comments
In the past my long read polishing pipeline was:
1 x racon followed by 1 x medaka
I was wondering if you have any data on potential combinations of polishing tools.
Is there anything nextpolish does better/worse than other polishing tools? Does it make sense to combine them or run nextpolish only?
Cheers,
Johannes
If you don't have short reads, I think medaka (long) is ok. If you have short reads, you can try medaka (long) + nextpolish (short) or nextpolish (long + short reads)
I ran a quick polisher combination comparison. In this case it looks like nextpolish followed by medaka (using long reads only) is the winner by a tiny margin.
Nice benchmark