Diamond 2.0.11

DIAMOND - Fast and sensitive protein alignment

DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:

  • Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST.
  • Frameshift alignments for long read analysis.
  • Low resource requirements and suitable for running on standard desktops or laptops.
  • Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

Location and version:

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$ which diamond
/local/cluster/bin/diamond
$ diamond version
diamond version 2.0.11

help message:

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$ diamond help
diamond v2.0.11.149 (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-valuesetting)
--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                enable tantan masking of repeat regions (0/1=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 frameof at least this length
--freq-sd                number of standard deviations for ignoring frequent seeds
--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 ahit (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                    Sequence numbers to display.

Online documentation at http://www.diamondsearch.org

DIAMOND is a near drop-in replacement for blastp+. One downside to DIAMOND is that the databases and the diamond executable are tied to one another -> databases need to be updated whenever the diamond executable is updated.

An updated NCBI nr for DIAMOND is found at /nfs1/CGRB/databases/NCBI/latest_diamond_DB/nr.dmnd.

software ref: https://github.com/bbuchfink/diamond
research ref: https://doi.org/10.1038/s41592-021-01101-x