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.