Provided by: diamond-aligner_2.1.8-1_amd64 
NAME
diamond - accelerated BLAST compatible local sequence aligner
DESCRIPTION
diamond v2.0.13.151 (C) Max Planck Society for the Advancement of Science Documentation,
support and updates available at http://www.diamondsearch.org Please cite:
http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
Syntax: diamond COMMAND [OPTIONS]
Commands: makedb Build DIAMOND database from a FASTA file blastp Align amino acid query
sequences against a protein reference database blastx Align DNA query sequences against a
protein reference database view View DIAMOND alignment archive (DAA) formatted file
help Produce help message version Display version information getseq Retrieve
sequences from a DIAMOND database file dbinfo Print information about a DIAMOND database
file test Run regression tests makeidx Make database index
General options: --threads (-p) number of CPU threads --db (-d)
database file --out (-o) output file --outfmt (-f) output format
0 = BLAST pairwise
5 = BLAST XML
6 = BLAST tabular
100 = DIAMOND alignment archive (DAA) 101 = SAM
Value 6 may be followed by a space-separated list of these keywords:
qseqid means Query Seq - id qlen means Query sequence length sseqid means Subject
Seq - id sallseqid means All subject Seq - id(s), separated by a ';' slen means
Subject sequence length qstart means Start of alignment in query qend means End of
alignment in query sstart means Start of alignment in subject send means End of
alignment in subject qseq means Aligned part of query sequence qseq_translated
means Aligned part of query sequence (translated) full_qseq means Query sequence
full_qseq_mate means Query sequence of the mate sseq means Aligned part of subject
sequence full_sseq means Subject sequence evalue means Expect value bitscore means
Bit score score means Raw score length means Alignment length pident means
Percentage of identical matches nident means Number of identical matches mismatch
means Number of mismatches positive means Number of positive - scoring matches
gapopen means Number of gap openings gaps means Total number of gaps ppos means
Percentage of positive - scoring matches qframe means Query frame btop means Blast
traceback operations(BTOP) cigar means CIGAR string staxids means unique Subject
Taxonomy ID(s), separated by a ';' (in numerical order) sscinames means unique
Subject Scientific Name(s), separated by a ';' sskingdoms means unique Subject
Super Kingdom(s), separated by a ';' skingdoms means unique Subject Kingdom(s),
separated by a ';' sphylums means unique Subject Phylum(s), separated by a ';'
stitle means Subject Title salltitles means All Subject Title(s), separated by a
'<>' qcovhsp means Query Coverage Per HSP scovhsp means Subject Coverage Per HSP
qtitle means Query title qqual means Query quality values for the aligned part of
the query full_qqual means Query quality values qstrand means Query strand
Default: qseqid sseqid pident length mismatch gapopen qstart qend sstart send
evalue bitscore
--verbose (-v) verbose console output --log enable debug log
--quiet disable console output --header Write header
lines to blast tabular format.
Makedb options: --in input reference file in FASTA format --taxonmap
protein accession to taxid mapping file --taxonnodes taxonomy nodes.dmp from
NCBI --taxonnames taxonomy names.dmp from NCBI
Aligner options: --query (-q) input query file --strand query
strands to search (both/minus/plus) --un file for unaligned queries
--al file or aligned queries --unfmt format of
unaligned query file (fasta/fastq) --alfmt format of aligned query file
(fasta/fastq) --unal report unaligned queries (0=no, 1=yes)
--max-target-seqs (-k) maximum number of target sequences to report alignments for
(default=25) --top report alignments within this percentage range of
top alignment score (overrides --max-target-seqs) --max-hsps maximum number
of HSPs per target sequence to report for each query (default=1) --range-culling
restrict hit culling to overlapping query ranges --compress compression for
output files (0=none, 1=gzip, zstd) --evalue (-e) maximum e-value to report
alignments (default=0.001) --min-score minimum bit score to report alignments
(overrides e-value setting) --id minimum identity% to report an
alignment --query-cover minimum query cover% to report an alignment
--subject-cover minimum subject cover% to report an alignment --fast
enable fast mode --mid-sensitive enable mid-sensitive mode --sensitive
enable sensitive mode) --more-sensitive enable more sensitive mode
--very-sensitive enable very sensitive mode --ultra-sensitive enable ultra
sensitive mode --iterate iterated search with increasing sensitivity
--global-ranking (-g) number of targets for global ranking --block-size (-b)
sequence block size in billions of letters (default=2.0) --index-chunks (-c) number
of chunks for index processing (default=4) --tmpdir (-t) directory for
temporary files --parallel-tmpdir directory for temporary files used by
multiprocessing --gapopen gap open penalty --gapextend gap
extension penalty --frameshift (-F) frame shift penalty (default=disabled)
--long-reads short for --range-culling --top 10 -F 15 --matrix
score matrix for protein alignment (default=BLOSUM62) --custom-matrix file
containing custom scoring matrix --comp-based-stats composition based statistics
mode (0-4) --masking masking algorithm (none, seg, tantan=default)
--query-gencode genetic code to use to translate query (see user manual)
--salltitles include full subject titles in DAA file --sallseqid
include all subject ids in DAA file --no-self-hits suppress reporting of
identical self hits --taxonlist restrict search to list of taxon ids
(comma-separated) --taxon-exclude exclude list of taxon ids (comma-separated)
--seqidlist filter the database by list of accessions --skip-missing-seqids
ignore accessions missing in the database
Advanced options: --algo Seed search algorithm
(0=double-indexed/1=query-indexed/ctg=contiguous-seed) --bin number of
query bins for seed search --min-orf (-l) ignore translated sequences without an
open reading frame of at least this length --seed-cut cutoff for seed
complexity --freq-masking mask seeds based on frequency --freq-sd
number of standard deviations for ignoring frequent seeds --motif-masking
softmask abundant motifs (0/1) --id2 minimum number of identities for
stage 1 hit --xdrop (-x) xdrop for ungapped alignment --gapped-filter-evalue
E-value threshold for gapped filter (auto) --band band for dynamic
programming computation --shapes (-s) number of seed shapes (default=all
available) --shape-mask seed shapes --multiprocessing enable
distributed-memory parallel processing --mp-init initialize multiprocessing
run --mp-recover enable continuation of interrupted multiprocessing run
--mp-query-chunk process only a single query chunk as specified --ext-chunk-size
chunk size for adaptive ranking (default=auto) --no-ranking disable ranking
heuristic --ext Extension mode (banded-fast/banded-slow/full)
--culling-overlap minimum range overlap with higher scoring hit to delete a hit
(default=50%) --taxon-k maximum number of targets to report per species
--range-cover percentage of query range to be covered for range culling
(default=50%) --dbsize effective database size (in letters)
--no-auto-append disable auto appending of DAA and DMND file extensions
--xml-blord-format Use gnl|BL_ORD_ID| style format in XML output --stop-match-score
Set the match score of stop codons against each other. --tantan-minMaskProb minimum
repeat probability for masking (default=0.9) --file-buffer-size file buffer size in
bytes (default=67108864) --memory-limit (-M) Memory limit for extension stage in GB
--no-unlink Do not unlink temporary files. --target-indexed Enable
target-indexed mode --ignore-warnings Ignore warnings
View options: --daa (-a) DIAMOND alignment archive (DAA) file --forwardonly
only show alignments of forward strand
Getseq options: --seq Space-separated list of sequence numbers to
display.
Online documentation at http://www.diamondsearch.org
AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.