USEARCH, UPARSE, What are they good at?

Question

[mhmtgenc85]

I have big NGS data includes amplicons of bacterial 16S rRNA . I would like to cluster them OTUs to species level. Can I use Usearch/uparse for it , if yes , how? Thanks in advance m fellow friends.

Answer 1

[archana.bioinfo87]

You can see this link for more detail http://qiime.org/tutorials/usearch_quality_filter.html

Hopefully it can help in what you want to do.

Answer 2

[5heikki]

You probably can but I would recommend cd-hit over them

[Steven Lakin]

I disagree. CD-HIT produces gappy alignments compared to USEARCH, since CD-HIT doesn't penalize gaps as much as USEARCH does. Rarely are interspersed false positive gaps preferred over false negative gaps or false positive gaps in series when meaningful alignments are the desired result, for example, which is why affine gap penalty exists.

http://drive5.com/usearch/cdhitv4_alignment95.html