USEARCH

120,000 new RNA virus species discovered by mining the SRA (paper).

Syncmers are better than minimizers (paper).

Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).

Open-source USEARCH
https://github.com/rcedgar/usearch12

USEARCH has been cited by
20,922 papers
Google scholar
Last updated 26 Jul 2024

GitHub

Download 32-bit

Features

UPARSE OTU clustering

Documentation

High-throughput search and clustering
USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

Improved productivity and insights
USEARCH combines many different algorithms into a single package with outstanding documentation and support. This cuts your learning curve, reduces the number of steps you need to take for a given task, and slashes compute times. USEARCH will encourage you to explore your data, enabling new insights and suggesting new analyses that you might not have tried with slower tools.

Free for most users
Licenses to use 32-bit USEARCH are offered at no charge for all users, including commercial. You can download the 32-bit version here.