DIAMOND(1)

📦 version 2.2.5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 DIAMOND(1) 💖

okay bestie, welcome to the DIAMOND(1) manual page — this is literally the whole vibe for diamond, the accelerated BLAST compatible local sequence aligner. no cap, we're gonna go through every flag, every command, every lil keyword, and you're gonna understand it. periodt. 💅✨

✨ NAME ✨

  • diamond — accelerated BLAST compatible local sequence aligner 🦋

💖 DESCRIPTION 💖

so first things first, the version is diamond v2.0.13.151, and the copyright is (C) Max Planck Society for the Advancement of Science. Documentation, support and updates are available at http://www.diamondsearch.org. Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x — that's Nature Methods (2021). iconic. 📝✨

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 ℹ️
  • 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 📋

output format values

  • 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. slay. 💅

so yeah, that's the whole page. the footer says diamond 2.0.13, October 2021, DIAMOND(1) — mwah 💋✨

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