USEARCH —— The simplest amplicon analysis process for Easy to learn
USEARCH official English homepage: http://www.drive5.com/usearch/
This site is authorized by USEARCH author Robert Edgar and translated by the "Metagenome" official account.
USEARCH Introduction
USEARCH is the best amplicon analysis process. It has realized nearly 200 common functions for amplicon analysis in software with a volume of only 1 MB. It is easy to install and run at a fast speed.
Figure 1. Screenshot of USEARCH article citation statistics (as of February 24, 2022, Google academic statistics citation 16,532 times)
Figure 1. USEARCH author Google academic homepage (as of February 24, 2022, 101,538 times)
USEARCH author is Robert Edgar independent researcher (Independent Investigator) has developed a series of classic algorithms and software in this field, such as the amplicon analysis process USEARCH[1] (cited 16,000 times), the chimera detection software UCHIME[2] (cited 11,000 times), the OTU clustering and representative sequence identification algorithm UPARSE[3] (cited 9,253 times), and the denoising algorithm UNOISE[4] for error filtering and correction of sequencing data. The introduction of these new algorithms and software has greatly improved the speed and accuracy of amplicon data analysis.
USEARCH not only has fast analysis speed, but also has strong software availability, which can effectively reduce the cost of introductory learning and save valuable time. For further reading, welcome to click on the link below to read the historical articles of the Metagenome official account about USEARCH.
Amplicon Analysis Artifact USEARCH Introduction to
USEARCH V11 new features introduction
USEARCH latest version v11 commands
OTU table drawing otutab_rare
core OTU identification otutab_core
USEARCH advantages
small size:
ml7QIIME system software size is G, while USEARCH only has 1M size to complete most analysis functions on the market;
is easy to install:
software has no dependencies, and after downloading, add the environment variable to run;
runs fast:
R language is too inefficient in front of big data. USEARCH is written in C, and the data processing speed is 20 times that of R.
identifies the core algorithm of ASV UNOISE3 is also 100 times faster than the mainstream software DADA2[5], and delbur is more than 10 times faster than [6]. For details, see the introduction and comparison of mainstream non-clustering methods dada2, deblur and unoise3;
Cross-platform:
Most software can only run on Linux.
USEARCH supports three major mainstream operating systems, not only running on Linux services, but also easily analyzing amplicon big data on your Windows/Mac notebook.
software download
2-bit version software download
32-bit version USEARCH free download for individual users, please visit the following address, self-service free application
http://www.drive5.com/usearch/download.html
professional version to purchase
USEARCH 64-bit version, divided into commercial version and academic version (a academic email is required).
commercial version, original price is $1,485 (~￥10,300 yuan), current price is 10,300 yuan, invoices and contracts (including taxes)
academic version, original price is $885 (~￥6,200 yuan), current price is 6,200 yuan, invoices and contracts (including taxes)
software supports three major mainstream systems, Linux / Mac OSX / Windows, you can choose one of your commonly used working environments.
purchases the professional version through the Chinese website and enjoys price discounts, which is convenient for invoice issuing units to reimburse, and at the same time enjoys the qualification for communication between Chinese professional and technical VIP groups and obtains professional answers.
Contact information
Email: Metagenome Official Account metagenome@126.com
WeChat: meta-genomes
Telephone: 17001263056
References
Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26:2460-2461.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R: UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
Edgar RC: UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature Methods 2013, 10:996.
Edgar RC, Flyvbjerg H: Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics 2015, 31:3476-3482.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP: DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 2016, 13:581.
Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, et al.: Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2017, 2:e00191-00116.
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