NAME

       diamond - accelerated BLAST compatible local sequence aligner

SYNOPSIS

       diamond COMMAND [OPTIONS]

DESCRIPTION

        DIAMOND is a sequence aligner for protein and translated DNA searches
        and functions as a drop-in replacement for the NCBI BLAST software
        tools. It is suitable for protein-protein search as well as DNA-protein
        search on short reads and longer sequences including contigs and
        assemblies, providing a speedup of BLAST ranging up to x20,000.

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

OPTIONS

   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

              sseq means Aligned part of 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)

              stitle means Subject Title

              salltitles means All Subject Title(s), separated by a '<>'

              qcovhsp means Query Coverage Per HSP

              qtitle means Query title

              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

   Makedb options:
       --in   input reference file in FASTA format

   Aligner options:
       --query (-q)
              input query file

       --un   file for unaligned queries

       --unal report unaligned queries (0=no, 1=yes)

       --max-target-seqs (-k)
              maximum number of target sequences to report alignments for

       --top  report   alignments   within   this   percentage   range   of   top   alignment  score  (overrides
              --max-target-seqs)

       --compress
              compression for output files (0=none, 1=gzip)

       --evalue (-e)
              maximum e-value to report alignments

       --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

       --sensitive
              enable sensitive mode (default: fast)

       --more-sensitive
              enable more sensitive mode (default: fast)

       --block-size (-b)
              sequence block size in billions of letters (default=2.0)

       --index-chunks (-c)
              number of chunks for index processing

       --tmpdir (-t)
              directory for temporary files

       --gapopen
              gap open penalty (default=11 for protein)

       --gapextend
              gap extension penalty (default=1 for protein)

       --matrix
              score matrix for protein alignment (default=BLOSUM62)

       --custom-matrix
              file containing custom scoring matrix

       --lambda
              lambda parameter for custom matrix

       --K    K parameter for custom matrix

       --comp-based-stats
              enable composition based statistics (0/1=default)

       --seg  enable SEG masking of queries (yes/no)

       --query-gencode
              genetic code to use to translate query (see user manual)

       --salltitles
              print full subject titles in output files

       --no-self-hits
              suppress reporting of identical self hits

   Advanced options:
       --min-orf (-l)
              ignore translated sequences without an open reading frame of at least this length

       --freq-sd
              number of standard deviations for ignoring frequent seeds

       --id2  minimum number of identities for stage 1 hit

       --window (-w)
              window size for local hit search

       --xdrop (-x)
              xdrop for ungapped alignment

       --ungapped-score
              minimum alignment score to continue local extension

       --hit-band
              band for hit verification

       --hit-score
              minimum score to keep a tentative alignment

       --gapped-xdrop (-X)
              xdrop for gapped alignment in bits

       --band band for dynamic programming computation

       --shapes (-s)
              number of seed shapes (0 = all available)

       --shape-mask
              seed shapes

       --index-mode
              index mode (0=4x12, 1=16x9)

       --fetch-size
              trace point fetch size

       --rank-factor
              include subjects within this range of max-target-seqs

       --rank-ratio
              include subjects within this ratio of last hit

       --max-hsps
              maximum number of HSPs per subject sequence to save for each query

       --dbsize
              effective database size (in letters)

       --no-auto-append
              disable auto appending of DAA and DMND file extensions

       --target-fetch-size
              number of target sequences to fetch for seed extension

   View options
       --daa (-a)
              DIAMOND alignment archive (DAA) file

       --forwardonly
              only show alignments of forward strand

   Getseq options
       --seq  Sequence numbers to display.

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.