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Output files for search and clustering commands

Hit selection options
The accept and termination options determine how many hits USEARCH will store internally before stopping the search for a given query sequence. Hit selection options determine which of the accepted hits will be written to the output files. See also weak hits. Hits are reported in order of decreasing identity (global) or decreasing alignment score (local).

Option   Description Option   Description
top_hit_only   Top hit only (break ties). cover_query   Sufficient hits to cover query.
top_hits_only   All top hits. mosaic   Mosaic cover of query.
maxhits N   At most N hits. uc_allhits   Show all hits in uc output file.
output_no_hits   Report queries with no hits.      

Output files

Most output files report hits, i.e. query-target alignments that meet the accept criteria. Any number of output files may be specified, enabling several different types of output to be generated from one run.

Option   Description Option   Description
alnout   Human-readable alignments. matched
  Queries that matched DB (FASTA or FASTQ).
userout   User-defined tabbed, see userfields. notmatched
  Queries that did not match DB (FASTA or FASTQ).
uc   UCLUST-format tabbed text. dbmatched   DB sequences that matched (FASTA).
fastapairs   Pair-wise alignments (FASTA). dbnotmatched   DB sequences not matched (FASTA).
centroids   Cluster centroids (FASTA). msaout   Multiple alignments of clusters (FASTA).
consout   Cluster consensus seqs. (FASTA). samout   SAM format.
blast6out   BLAST tabbed format. nastout   NAST format.
qsegout   Query segments (FASTA). tsegout   Target segments (FASTA).
clusters   Directory to store FASTA files, one per cluster (cluster_fast only).