Usearch in PCR - Search localsearch

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HomeAboutContact Open-source USEARCH Download latest release Download older binaries Source code at GitHub OTU / ASV analysis Documentation USEARCH papers ReseekStructure alignment and search More accurate than TM-align,

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https://www.drive5.com/usearch/manual/

USEARCH - drive5

OTU and denoising analysis for 16S, ITS etc. Recommended procedures Example scripts and tutorials Errors and biases in amplicon sequencing Old manuals Version 10 Version 9.2 Version 8.1 Version 7 Version 6 Support Technical support Known bugs Publications Papers and how to cite USEARCH

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https://www.drive5.com/usearch/manual/cmds_all.htm…

USEARCH - drive5

usearch_global Fast database search using global alignment usearch_local Fast database search using local alignment Taxonomy commands calc_lcr_probs Calculate Lowest Common Rank probabilities from dist. matrix with taxonomy makeudb_sintax Make UDB database file for sintax nbc_tax Predict taxonomy using RDP Naive Bayesian Classifier algorithm

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USEARCH - drive5

USEARCH algorithm The USEARCH algorithm searches a database for high-identity hits to one or more database sequences ("targets"). USEARCH is used by the usearch_global and usearch_local commands and is used as a subroutine by cluster_fast and cluister_smallmem . This algorithm is fundamentally different from the UBLAST algorithm that is designed for low identity local searches. Recommended ...

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USEARCH - drive5

USEARCH is distributed as one file, known as the binary file or executable file. It is completely self-contained: it does not require configuration files, environment variables, third-party libraries or other external dependencies.

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https://www.drive5.com/usearch/manual/cmdline.html

USEARCH - drive5

USEARCH command line A typical USEARCH command line looks like this: usearch -cluster_fast seqs.fasta -id 0.9 -centroids nr.fasta | | | | | | | Command Input filename | Output option with filename Binary filename Parameter option(s) The command line starts with the binary filename. In this manual, examples are always shown using 'usearch' as the filename. You should use the actual name of your ...

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https://www.drive5.com/usearch/manual/topics.html

USEARCH - drive5

USEARCH software installation and use Installing USEARCH Command line USEARCH binary file name Memory use and 32 / 64-bit binaries Installing multiple USEARCH versions Known bugs Commentaries and rebuttals QIIME v1 grossly over-estimates mock community diversity Analysis of Brown 2017 ITS mock data Problems with CD-HIT sequence identities

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https://www.drive5.com/usearch/manual8.1/

USEARCH manual - drive5

usearch_global, usearch_local ublast, search_global, search_local, search_exact, search_pcr, search_oligodb, search_peptidedb Indexed databases: makeudb_usearch, makeudb_ublast, udbstats, udbinfo, udb2fasta Taxonomy assignment: utax, cluster_otus_utax Chimera filtering and classification: uchime_ref, uparse_ref, uchime_denovo FASTA/Q file ...

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https://www.drive5.com/usearch/manual/pipe_otutab.…

USEARCH - drive5

An OTU table is created by the otutab command . Input should be reads before quality filtering and before discarding low-abundance unique sequences, e.g. singletons. This will improve sensitivity, because many low-quality and low-abundance reads will map successfully to OTUs. Reads must have sample indenfiers in the labels. The search database is the OTU (or ZOTU) sequences, which must have ...