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aaout Translated ORFs, FASTA format.
abskew Min abundance skew.
accel Accel parameter for UBLAST.
acceptall Accept all hits.
alnout Hits as human-readable alignments.
band Min band width.
blast6out Hits in -outfmt 6 BLAST+ output (same as -m8 for older BLAST).
ccnodesout Connected component (one line per node).
ccout Connected compontents (one line per cluster).
centroids Cluster centroid sequences in FASTA format.
chimeras Sequences classified as chimeric in FASTA format.
chunks Number of chunks.
clusterout Cluster output file, tabbed text, clusternr+label.
clusters Clusters in tabbed text format.
consout Output filename prefix, consensus sequences.
cover_query Report sufficient hits to cover query sequence.
db Database filename
dbaccelpct Database accel parameter.
dbmask Database masking (none, seg, dust, fastamino, fastnucleo, soft).
dbmatched Database sequences that matched at least one query.
dbnotmatched Database sequences that did not match a query.
dbstep Database step parameter.
default_size Default size for sortbysize.
discarded_labels Labels of discarded low-complexity sequences.
distmi Distance measure (id, sim).
distmo Distance measure (id, sim).
distmx_brute Brute-force calculation of distance matrix.
distmxout sparse distance matrix.
distmxoutout Hits for search_pcr.
dn Pseudo-count prior.
eeout Append "ee=X;" expected errors annotation to read labels.
eetabbedout Output file, expected errors in tabbed text format.
evalue Max E-value.
fastaout FASTA output from some commands.
fastaout_notmerged_fwd Unmerged fwd reads (FASTA format).
fastaout_notmerged_rev Unmerged rev reads (FASTA format).
fastapairs Hits as pair-wise alignments in FASTA format.
fastapairs_dots Replace identities with dots in query sequence.
fastq_allowmergestagger Allow 'staggered' merges.
fastq_ascii ASCII base value for Q scores.
fastq_format Format of FASTQ file (ill, 454, pacbio, ion)
fastq_label_suffix Suffix appended to label of merged reads.
fastq_maxdiffs Max number of differences allowed in overlap for merging.
fastq_maxee Max expected errors in FASTQ read.
fastq_maxmergelen Max length allowed for merged read.
fastq_minlen Min length of FASTQ read after filtering.
fastq_minmergelen Min length allowed for merged read.
fastq_minovlen Min overlap of read pair for merging.
fastq_qmax Max Q score allowed by FASTQ format.
fastq_qmaxout Max Q score allowed by FASTQ format (output files).
fastq_qmin Min Q score allowed by FASTQ format.
fastq_stripleft Discard this number of bases at start of FASTQ read.
fastq_tail Min number of bases in a FASTQ tail.
fastq_trunclen Truncate FASTQ at this length.
fastq_truncqual Truncate FASTQ read at first base with Q<=fastq_truncqual.
fastqout Output file, FASTQ format.
fastqout_notmerged_fwd Unmerged fwd reads (FASTQ format).
fastqout_notmerged_rev Unmerged rev reads (FASTQ format).
format Format for sparse distance matrix.
fulldp Ignore hits with 100% identity.
gaforce Force global alignment even if HSPs are below threshold.
gapext String specifying gap extension penalty(ies).
gapopen String specifying gap open penalty(ies).
hardmask Mask by replacing letters with wildcard (N or X).
hspw Word length for HSP finding.
id Min identity (0.0 to 1.0) for search.
idprefix Min number of identical bases at start of alignment.
idsmoothwindow Window size for %id smoothing.
idsuffix Min number of identical bases at end of alignment.
join_padgap Letters to use for FASTQ join padding, default NNNNNNNN.
ka_dbsize Effective database size.
ka_gapped_k K for gapped alignments.
ka_gapped_lambda Lambda for gapped alignments.
ka_ungapped_k K for ungapped alignments.
ka_ungapped_lambda Lambda for ungapped alignments.
label Sequence label.
label_substr_match Use substring matching for sequence labels.
labels Input file, text format containing sequence labels.
leftjust Reject hit if terminal gaps at start of alignment.
lext Gap extend penalty for local alignments.
linebuff Max length of a line in an input file.
linkage Linkage type for agglomerative clustering (min, avg or max).
log Log file for informational messages.
log_used_opts Report all used options in log file.
lopen Gap open penalty for local alignments.
match Match score.
matched Query sequences that matched the database.
matrix Input filename, substitution matrix in BLAST format.
maxaccepts Max number of accepts.
maxamp Max amplicon length (search_pcr).
maxdiffs Min number of diffs (subs+gaps) in the alignment.
maxgaps Min number of gapped columns in the alignment.
maxhits Max number of hits to report for one query.
maxid Max identity (0.0 to 1.0) for hit.
maxp Max number of parents to consider.
maxqt Max query/target length ratio.
maxrejects Max number of rejects.
maxseqlength Max seqlence length (sortbylength).
maxsize Min cluster size.
maxsl Max shorter/longer length ratio.
maxsubs Min number of substitutions in the alignment.
mid Min match identity (0.0 to 1.0) for search.
min_cons_pct Min conservation for consensus sequence.
min_sizeratio Min size ratio.
min_unmasked_pct Min fraction of sequence left unmasked.
minamp Min amplicon length (search_pcr).
minchunk Min chunk size.
mincodons Min number of codons in an ORF.
mincols Min number of columns in the alignment.
mindiffs Mininum diffs to allow on each side of cross-over.
mindiv Min chimera divergence.
mingroupsize Min group size (rarefaction).
minh Min chimera score.
minhsp Min length of HSP.
minqt Min query/target length ratio.
minseqlength Min sequence length (sortbysize output).
minsize Min cluster size.
minsl Min shorter/longer length ratio.
minuniquesize Min cluster size.
mismatch Mismatch score.
mosaic Report mosaic hits.
mosaic_minseg Min segment size.
msaout Output filename prefix, multiple alignments.
nast_delgap Character to use for deletion gap in NAST output.
nast_locgap Character to use for unaligned sequence gap in NAST output.
nast_padgap Character to use for padding gap in NAST output.
nast_termgap Character to use for terminal gap in NAST output.
nastout Hits in NAST format.
nonchimeras Sequences not classified as chimeric in FASTA format.
notmatched Query sequences that did not match the database.
notrunclabels Don't truncate sequence labels.
nousort Don't use U-sort heuristic.
ntout Nucleotide ORFs, FASTA format.
orfstyle Options for ORF detection.
otu_radius_pct Radius for OTU clustering.
otus OTU representative sequences in FASTA format.
output Output filename
output_no_hits Report queries with no hits.
pattern Pattern for spaced alignment seeds.
pcrout Hits for search_pcr.
prefix Output filename prefix, clusters.
qmask Query masking (none, seg, dust, fastamino, fastnucleo, soft).
qsegout Query sequence hit segments in FASTA format.
qualout Append "qual=" Q score annotation to FASTA read labels.
query_cov Min fraction of query covered by alignment.
quiet Show only errors and warning messages on the terminal.
randseed Integer seed for random number generator.
relabel Re-label input sequences in output files.
reverse Input filename, reverse reads for merging.
rightjust Reject hit if terminal gaps at end of alignment.
rowlen Length of alignment row for -alnout.
sam_softclip Use SAM soft clipping.
samout Hits in SAM format.
sample_pct Sample fraction for sub-sampling.
sample_size Sample size for sub-sampling.
self Ignore hits with same label.
selfid Ignore hits to identical sequence.
show_termgaps Show terminal gaps in alnout.
sizein Count "size=N;" annotations towards cluster sizes.
sizeout Add "size=N;" annotations to cluster centroid labels.
slots Number of index slots.
sort Sort order (length or size)
sortedby Sort order (length, size, other)
sparsemx_minid Min identity to keep in sparse distance matrix.
strand Strand for nt search (plus or both).
strict_newick Convert labels that don't conform to Newick specification
subseq_end End of subsequence (1-based coordinate).
subseq_start Start of subsequence (1-based coordinate).
target_cov Min fraction of target covered by alignment.
termid Terminate search if identity < termid.
threads Number of threads (default: one per core).
top_hit_only Report only top hit (ties broken systematically).
top_hits_only Report only top hits (including ties).
topn Output only the first topn sequences (sortbysize, sortbylength).
tree Input filename for tree in Phylip format.
treeout Output filename for tree in Phylip format.
trunclen Truncate length.
tsegout Target sequence hit segments in FASTA format.
uc Top hit/centroid assignment in uc format.
uc_allhits  (No longer supported).
uchime_abno A=B, Q different is no vote.
uchime_countgapends Count end gaps as differences.
uchimealns UCHIME alignments.
uchimeout UCHIME output.
uparse_annot_maxdivqm Max divergence between query and model.
uparse_break Chimeric breakpoint score for UPARSE-REF d.p.
uparse_match Match score for UPARSE-REF d.p.
uparse_maxhot Max nr of candidate parents to consider.
uparse_mismatch Mismatch score for UPARSE-REF d.p.
uparsealnout UPARSE alignment output.
uparseout Output file, UPARSE tabbed format.
userfields Fields to appear in -userout file.
userout Hits in tabbed text as specified by -userfields.
weak_evalue Max E-value for weak hit.
weak_id Min identity for weak hit.
wordlength Word length for indexing.
xa Abstain vote weight.
xdrop_g X-drop parameter for gapped alignments.
xdrop_nw X-drop parameter for HSP-finding.
xdrop_u X-drop parameter for ungapped alignments.
xn No vote wight.
xsize Delete "size=N;" annotations.