|
Option |
|
Description |
|
‑alnout filename |
|
Human-readable
alignments. |
|
‑userout filename |
|
Tab-separated text file, fields are
specified by -userfields. |
|
‑uc filename |
|
Tab-separated text file with records for
hits and clusters. |
|
‑fastapairs filename |
|
FASTA file. Each pair of sequences is a
hit with the query first then the target, with gaps inserted to
align them. |
|
‑centroids
filename |
|
FASTA file for
cluster centroid
sequences. |
|
‑consout filename |
|
FASTA file for
cluster consensus
sequences. Note that this option may use a
substantial amount of memory. |
|
‑blast6out filename |
|
Tab-separated text file compatible with
the NCBI BLAST m8 and outfmt 6
formats. |
|
-matched filename |
|
FASTA file containing
query sequences that matched the database. Supported by v6.0.229 and later. |
|
-notmatched filename |
|
FASTA file containing
query sequences that did not match the database. Supported by v6.0.229 and
later. |
|
-dbmatched filename |
|
FASTA file containing
database sequences matched to at least one query sequence. Supported by v6.0.229 and later.
If -sizeout is specified, the number of queries that matched this sequence is
written as a size annotation. |
|
-dbnotmatched filename |
|
FASTA file containing
database sequences that were not matched to a query sequence. Supported by v6.0.229 and
later. |
|
-msaout filename |
|
FASTA file containing
a multiple alignment of each cluster. Supported by v6.0.307 and later. Note that
this option may use a substantial amount of memory. |
|
-clusters prefix |
|
Creates one FASTA file for
each cluster. The filename is constructed by appending the cluster number 0, 1,
2... to prefix. Since the number of clusters may be large, it is
suggested to use a directory name in the prefix, e.g. -clusters clusterdir/cluster_.
You must create the directory before running usearch.
Note that this option may use a substantial amount of memory. |