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). |