NUCmer

[benjaminversteeg]

Dear reader,

The Bioinformatics branch is well known for its high speed of development. The founding of NUCmer has been some while now (I believe somewhere around the 1999s) That's why I was wondering whether the application isn't somewhat outdated. I made some attempts to find reviewing papers, with not much succes. Therefor I hereby make a request to inform me in this case according to your experiences.

Thank you

[Melissa]

Not sure if I understand your question correctly. Here's my opinion on Mummer. It's not updated for a few years. However, I wouldn't call it outdated because many bioinformatians I know including myself are still using Mummer. It seems like there is no software out there that can replace all of its fuctions completely.

[flxlex]

I second that. In fact, now that reads are getting longer, and assemblies more complete, the Mummer package is more popular than ever.

That doesn't mean there isn't room for a new program, for example one that outputs the currently popular formats (BAM, BED etc).

[nickschurch]

That doesn't mean there isn't room for a new program, for example one that outputs the currently popular formats (BAM, BED etc).

That would be very useful - any takers?