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. | 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
matchedfq |
Queries that matched DB (FASTA or FASTQ). | ||
| userout | User-defined tabbed, see userfields . |
notmatched
notmatchedfq |
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). |