Max length for derep or cluster commands

[ekar...@gmail.com]

Dear Torbjorn and colleagues

Thank you for maintaining the group.

Are there any recommended upper-length limits for the sequences fed for the derep-full-length or clustering methods? Is it recommended to use these commands for sequences that are a few thousand bp long?

Many thanks in advance

[Torbjørn Rognes]

Hi

There is no hard limit, but generally VSEARCH may be slow when using sequences that are longer than 5000 bp when these sequences need to be exhaustively aligned. Dereplication is not affected by this, but clustering may be affected.

- Torbjørn

[ekar...@gmail.com]

Thank you.