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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.

UPARSE tutorial video posted on YouTube. Make OTUs from MiSeq reads.



usearch_global command

Search for one (default) or a few high-identity hits to a database using the USEARCH algorithm. Alignments are global. To get more than one hit, increase -maxaccepts (see accept options).

An identity threshold must be specified using the -id option. If full-length, exact matches are required, then it is better to use search_exact than usearch_global with -id 1.0.

The query file may be in FASTA or FASTQ format.

A database file must be specified using the -db option. FASTA and .udb formats are supported. For large databases, .udb format is recommended (see makeudb_usearch command).

The -strand option is required for nucleotide databases.

Nucleotide, protein and translated searches are supported.

See also
  Output files
Accept options
  Weak hits
  Termination options
  Indexing options
  Masking options
  Alignment parameters
  Alignment heuristics


usearch -usearch_global query.fasta -db proteins.udb -id 0.8 -alnout hits.aln
usearch -usearch_global reads.fastq -db ESTs.fasta -id 0.9 -blast6out hits.b6 \
  -strand plus -maxaccepts 8 -maxrejects 256